bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

SIANN: Strain Identification by Alignment to Near Neighbors

Samuel S. Minot, Stephen D. Turner, Krista L. Ternus, and Dana R. Kadavy

January 9, 2014

Abstract Next-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifically designed to rapidly detect a set of target organisms in mixed samples that achieves a high degree of species- and strain-specificity by aligning short sequence reads to the genomes of near neighbor organisms, as well as that of the target. Empirical benchmarking alongside the current state-of-the-art methods shows an extremely high Positive Predictive Value, even at very low abundances of the target organism in a mixed sample. SIANN is available as an Illumina BaseSpace app, as well as through Signature Science, LLC. SIANN results are presented in a streamlined report designed to be comprehensible to the non-specialist user, providing a powerful tool for rapid species detection in a mixed sample. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.

Introduction There are many different methods that characterize the mixture of organisms present within a metagenomic dataset. Such datasets are generated when a complex environmental sample is processed by a “next-generation” high-throughput genome sequencing protocol, and they consist of large numbers of short nucleotide sequences. Each sequence represents a small fragment of a randomly selected genome from the very large collection of genomes present in the source sample. Those sequences indicate the presence of one organism or another according to their similarity to a set of known reference genomes. While a given sequence may be unique to one species, it also may be found in diverse organisms across the tree of life. Therefore, one analytical challenge (among many) is to take that collection of sequences (likely numbering in the millions) and accurately determine what species are present in the sample. Here we describe a novel method (SIANN: Strain Identification by Alignment to Near Neighbors) that is specifically designed to rapidly detect a set of targeted organisms from a metagenomic dataset by aligning reads to genomic regions that are unique at the strain or species level. bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

The analytical question motivating a particular piece of metagenomic bioinformatic analysis may vary widely by user and sample type (Segata, et al., 2013). For example, the function of the human gut microbiome may depend on the relative abundance of hundreds of species of bacteria and the types of metabolic genes they contain (Wu, et al., 2011; Schloissnig, et al., 2013). In contrast, the clinical treatment of a patient may depend on whether or not a particular virus, or a consortium of co-infecting pathogens, is/are detected in their blood. It is this second class of presence/absence questions that SIANN is designed to address. SIANN is appropriate for situations in which a user wants to know whether a particular organism or set of organisms is present in a sample, but isn’t interested in the functions encoded in their genomes, the relative abundance of each organism, or any other more in-depth analysis.

Methods

Approach Metagenomic classification methods are based on a wide variety of theoretical underpinnings. The basic varieties include alignment of reads to various nucleotide databases or exact matching to nucleotide or protein signature sequences (or kmers). A representative set of recent methods are described in Table 1 (also see Bazinet & Cummings 2012).

Name Method Reference MEGAN Alignment to large nucleotide database Huson, et al., 2011 PhymmBL Alignment to large nucleotide database Brady & Salzberg, 2011 with interpolated Markov models Metaphyler Alignment to clade-specific marker genes Liu, et al., 2011 MetaPhlAn Alignment to clade-specific marker genes Segata, et al., 2012 LMAT Nucleotide kmer matching Ames, et al., 2013 Kraken Nucleotide kmer matching Wood & Salzberg, in submission Sequedex Protein kmer matching Berendzen, et al., 2012 mOTU Alignment to universal marker genes Sunagawa, et al., 2013 Phylosift Insertion into reference nucleotide and Darling, et al., in protein alignments preparation Table 1. Summary of methods for metagenomic classification.

Overall, these methods are designed to either classify individual reads to, and/or predict the total abundance of, clades (e.g. genus or species) across the entire tree of life. They generally require reference databases that are very large and/or require a large amount of processing to generate. The gap SIANN is designed to fill is when the entire tree of life is irrelevant, and only predefined subsets of organisms need to be detected. For an underlying method we chose read alignment to diagnostic genomic regions because the algorithms for read alignment are highly parallelizable and have been optimized heavily by the community at large (the current implementation of

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SIANN uses bowtie2 [Langmead & Salzberg, 2012] for the alignment function, but can be adapted to any alignment algorithm). This approach is distinct from using clade- specific marker genes (Segata, et al., 2012) because unique regions that are larger, smaller, or outside of genes can also be used. Furthermore, this approach supports the rapid construction of custom databases using reference genome sets that require only minimal user-supplied structure.

To understand the principle at work, consider a set of reads that have been aligned to the genomes of several strains belonging to two species. Some regions of those genomes are species-specific, some are strain-specific, and some are shared (Figure 1a). When a set of reads is aligned to those genomes such that each read is placed in as many locations as it has a match (at a reasonably stringent threshold), visual inspection of the distribution of reads yields an intuitive understanding of the true source organism as Species I/Strain B (Figure 1b). If Strain B were not present in the reference database, it would still be clear that the organism was an unknown strain of Species I.

A B

Figure 1. A) For a group of strains belonging to two different species, some regions may be unique to each species (region 1), while other regions may be unique to strains within each species (regions 2 and 3). B) A set of reads are aligned to these genomes, and the ones that align in a species- or strain-specific manner are identified by the combination of genomes to which they align. In this example, Strain B of Species I is the organism identified.

The unique identification of a species or strain is quantified by the proportion of the genome that is determined to be species- or strain-specific (defined as reads that are aligned to regions that are species- or strain-specific). Each species and strain is then assigned a numerical measure of the proportion that is covered by these diagnostic reads, and that proportional measure is compared to the ideal case, where sequences from a single organism (generated in silico) are aligned against the database in an identical manner. After that normalization factor is applied, the resulting score indicates whether the source sample contained any of the organisms in the reference database.

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The analysis is conducted independently on both the species and the strain level, so that if the true strain is not present in the database, the species of origin will still be identified. While many methods consider the complete taxonomic tree and assign reads to the least common ancestor, SIANN considers only two taxonomic levels: species and strain, throwing out anything that is not unique at one of those levels and thus obviating many of the confounding factors introduced by manually curated taxonomies.

The example shown in Figure 1b indicates that species-specific reads are identified as reads that align to one species (Species I, in that case) but not the other. If Species II were not present in the example shown in Figure 1b, a much larger number of reads would be assigned as “species-specific,” when in fact those regions are shared with other species. Therefore, the ability of this method to identify strain- and species-specific sequences is a direct function of the inclusion of near neighbors in the reference database. This characteristic is shared among many classification algorithms, but it is of particular note for this method when users have an opportunity to construct their own database.. In order to detect a target species with a high degree of specificity (reducing false positives), it is necessary to include other related species in the reference database. Only by parallel alignment to those near neighbors can the redundant sequences be separated from the species-specific ones. For example, in order to detect Bacillus anthracis in a sample, it would be necessary to include other species of Bacilli in the reference database so that the presence of B. cereus or B. thuringiensis in a sample does not lead to a false call for B. anthracis.

The nomenclature of genus, species, and strain is potentially problematic because it does not correspond to a consistent degree of evolutionary distance or genomic distinctiveness. The ability to distinguish two organisms by any method using genomic sequence data is proportional to the amount of each genome that is shared or unique. One might assume that any two organisms of the same species will have a relatively predictable amount of shared genomic identity. However, some pairs of organisms from the same species may have less in common than other pairs of organisms from different species or even genera. This ambiguity impacts SIANN in two ways. If two organisms have very little genomic sequence to distinguish them, the sensitivity of SIANN to detect either one will diminish (the rate of false negatives will increase as the likelihood of sequencing unique regions decreases). Conversely, if an organism is extremely dissimilar to the near neighbors selected for the database, the specificity with which SIANN detects that organism will decline (the rate of false positives will increase as the number of related genomes available in the database decreases). For example, if a database contained only E. coli and B.anthracis, a sample containing B. cereus would be misidentified as contraining B. anthracis. In the intended use case, a database targeting B. anthracis would contain B. cereus and a number of other near neighbors to prevent that kind of misidentification. It would be convenient to say that

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an ideal database can be made by calculating the ideal genetic distance between all references and then finding an ideal set of organisms to make up that database, but the behavior of any database will be governed by the particular genomes of the organisms it encounters in the wild. Because not all organisms evolve in the same manner (differences in mutation rate, horizontal gene transfer, recombination, etc), the suitability of a database and method to detect a given organism can only be determined by thorough validation and benchmarking, as well as updating the reference database as needed. Users of SIANN may construct their own custom databases to include newly identified genomes or specific subsets of genomes that best suit their research interests.

Steps to construct a custom database:

1. Select a set of target organisms 2. Gather a set of genome sequences for those target organisms as well as a matched set of near neighbors 3. Using those reference genome sequences as an input, SIANN will: a. Construct a reference index for alignment b. Simulate a set of reads from each genome c. Align each of those simulated read sets to all of the reference genomes d. Calculate the proportion of each reference genome that is strain- or species-specific e. [If two organisms do not have a minimal amount of unique sequences that exceeds the rate of sequencing error, SIANN asks that all but one of those organisms are removed from the database to eliminate redundancy. Note that the user can provide a single representative genome with multiple strain names so that the redundant strain names are not lost.]

The files contained within each SIANN database are a compressed genomic index and a list containing the proportion of each reference genome that was found to be strain- or species-specific during database construction.

To run SIANN:

1. Select a pre-made SIANN database and a set of sequences to be analyzed, and 2. SIANN will: a. Align each of the reads against the reference genomes b. Calculate the proportion of each reference genome that is strain- or species-specific within those reads c. Compare that proportion to the simulated ideal case generated during database creation

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d. Calculate the probability that the given results could be generated by random chance e. Report the normalized proportion and non-parametric statistic of likelihood for each strain and species in the reference database. The normalized proportion of the genome covered by strain- or species- specific reads is the primary statistic reported by this tool.

Benchmarking The performance of SIANN (version 1.6) was tested in comparison to the following state- of-the-art metagenomic classification programs: LMAT (version 1.2), MetaPhlAn (version 1.7.7), and Kraken (version 0.9.1b). All of the programs in Table 1 were investigated for this effort, and three were chosen based on their ability to run on our high-performance computing cluster with an execution time and memory requirement that would be suitable to a clinical lab. Each program was run on a set of 600 simulated datasets generated by MetaSim (Richter, et al., 2008). Each dataset consisted of 15,000,000 reads (100bp single-ended) with Illumina-simulated error (fourth-degree polynomial) (Korbel, et al., 2009). The 600 datasets were broken into 12 sets of 50 replicates. Each of the 12 sets contained organisms at different levels of abundance as shown in Table 2. Organisms were specifically chosen in pairs so that the ability to distinguish these near neighbors could be determined. The abundances were staggered at 4-fold intervals so that a wide range could be evaluated. All known species of near neighbors for each of

Organism 1 2 3 4 5 6 7 8 9 10 11 12 Bacillus 0.074% 0.30% 1.2% 4.7% 19% 76% anthracis Bacillus 0.074% 0.30% 1.2% 4.7% 19% 76% cereus Hanta virus 1.2% 4.7% 19% 76% 0.074% 0.30% Rift valley 0.30% 1.2% 4.7% 19% 76% 0.074% fever virus Clostridium 19% 76% 0.074% 0.30% 1.2% 4.7% botulinum Clostridium 1.2% 4.7% 19% 76% 0.074% 0.30% difficile Listeria 0.074% 0.30% 1.2% 4.7% 19% 76% fleischmann eii Listeria 4.7% 19% 76% 0.074% 0.30% 1.2% monocytog enes Monkeypox 1.2% 4.7% 19% 76% 0.074% 0.30% virus Vaccinia 19% 76% 0.074% 0.30% 1.2% 4.7% virus Yersinia 19% 76% 0.074% 0.30% 1.2% 4.7% enterocolitic a Yersinia 76% 0.074% 0.30% 1.2% 4.7% 19% pestis

Table 2. The abundance of each target organism in each set of simulated datasets. Each set is indicated by the number in the top row, and was generated with 50 replicates.

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the 12 target organisms were included in the reference database used by SIANN for this benchmarking (“Target Pathogen Database”) and are shown in Appendix 1.

Each program outputs a distinct measure. Kraken and LMAT both count the reads assigned to each taxon, MetaPhlAn calculates the abundance, and SIANN outputs a measure of the proportion of diagnostic genomic regions present. To put these measures on an even footing, we empirically calculated the false positive rate for each method over all 600 samples, at each possible measure of output. Because each dataset is made up of known organisms, any result can be classified as true or false. Therefore, for any possible result (say, 513 reads classified by LMAT or 1.6% abundance assigned by MetaPhlAn), one can calculate the proportion of calls with at least the same amount of support that were correct (True Positives/[True Positives+False Positives]), over all of the 600 datasets. That measure is commonly given as Positive Predictive Value (PPV). For each program, the results can be translated from the raw value into a PPV that is based on this empirical measure of error. The key item of interest is the PPV value for the results that we know to be true positives, the defined spike organisms. Another way of describing this approach is to say that the results of each program have been normalized to the false positive error rate that was empirically observed. If another set of samples were generated, the PPV vs. raw value curve (Figure 2) would likely fall differently, but in this case it gives us a means of comparing a diverse set of methods against the same ground truth. If method 1 detects an organism with a higher PPV than method 2 does, it means that method 1 has fewer false positives in the range that it reports true positives, which is the definition of utility in this setting.

For each method, PPV was calculated as a function of raw output value. Briefly, this was done by compiling the output for all 600 samples, labeling each result as false or true based on the sample set that it came from, and then calculating (at each possible value of output) what the proportion of TP/[TP+FP] was for results with at least that level of raw output. Some simplification steps were taken, such as focusing on the species- level assignments (for comparison with methods that do not perform strain assignment), and only taking the top hit for each species from each dataset. Custom R and BASH scripts were used for the data compilation and analysis.

Results The relationship of raw output value to PPV is shown for each of the four methods in Figure 2. The point at which PPV is very close to 1 (where 95% of results are true positives) is ~41,000 reads for Kraken, ~2,800 reads for LMAT, ~38% abundance for MetaPhlAn, and 0.21 for SIANN. For SIANN this means that having 38% of the species-unique genome covered by reads resulted in the vast majority of calls being accurate.

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Figure 2. Relationship of reported value for each program (horizontal axis, log scale) to the empirically-determined Positive Predictive Value (PPV), shown on the vertical axis. While the exact values depend on the test data used, the general values at significant cutoff values (0.8, 0.9, 0.95 PPV) remain relatively constant across different datasets (data not shown).

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For read- assignment methods (such as LMAT and Kraken), manual inspection of the results may yield a different understanding of confidence than is presented here, or in any automated analysis. For example, while each read that is assigned by LMAT and Kraken fall above a certain cutoff for species- specificity, some individual reads may be much more specific than others. One could identify a read that Figure 3. The Positive Predictive Value (PPV, vertical axis) is aligns to a single shown for each organism (boxes on right), at each level of species of bacteria known abundance (horizontal axis, see Table 2), and each with 100% accuracy program (boxes at top), across a maximum of 50 replicates over its 300bp (indicated by the size of each point). Note that the reference length, with the next database for MetaPhlAn does not include viruses, and the closest match being reference database for Kraken does not include RNA viruses only 90% similar. It is extremely(e.g., Hanta unlikely virus). that a 300bp exact match would arise due to random chance, and so the user could say with confidence that the organism of interest is found within the sequence data (not considering contamination, horizontal gene transfer, etc). However, such an approach is not currently implemented in an automated method, and many of the steps needed to make that assertion are performed manually by a domain expert, including alignment to near neighbors and ensuring that the read does not fall within a transposon, plasmid, etc. Therefore, while one could say that a single read is all that is needed to state with high PPV that an organism is present, the amount of reads assigned in an automated manner needed to achieve that level of PPV will number in the thousands (Fig 2).

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The next phase of benchmarking was to determine how many raw input reads were needed to achieve the threshold for high PPV. To demonstrate this we plotted the known abundance of each spike organism against the PPV value generated by each method (Figure 3). Each point (an organism at a known level of abundance) is comprised of a maximum of 50 replicates, where the diameter of each point increases with an increasing number of replicates. For demonstration purposes we are showing two pairs of bacteria and three viruses. Recall that for each of the pairs of bacteria (and the two poxviruses) any sample containing one did not contain the other (as shown in Table 1). The empty boxes result from the organisms not being called at any abundance. For MetaPhlAn, that is a result of no viruses being included in the version of the reference database available for this analysis. Kraken assigned no reads to Hanta virus because viral RNA genomes were not included in this version of the reference database (personal communication with D. Wood). This emphasizes the point that a) the ability to create custom databases targeting organisms of interest can be valuable, and b) the performance of any method must be benchmarked against each potential target of interest.

All methods were able identify the bulk of organisms in their databases at high abundances (75% and 18%, Figure 3), however performance varied considerably at lower abundances and depended on the particular organism and method used. SIANN detected each organism at high confidence, even at levels as low as 0.3% and 0.07% of the total.

Discussion The process of detecting trace amounts of a specific organism in a complex mixture of DNA is challenging enough for an expert, but that pales in comparison to the difficulty of accomplishing the same certainty of detection in an automated manner. The results presented here show that SIANN rapidly detects the presence of a given set of organisms with a high degree of specificity and sensitivity. For example, at the 95% confidence (PPV) cutoff of 0.2, SIANN reliably detects all of the organisms tested here at as low as 0.3% abundance. This strong performance is likely due to the fact that SIANN is able to use a method (read alignment to whole genomes) that would be far too computationally costly if it were applied to the entire collection of known genomes. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.

SIANN is available on Illumina’s BaseSpace (www.basespace.illumina.com) as a NativeApp, with the database tested here (Appendix 1), as well as a database made from the NCBI representative set of prokaryotic genomes (ftp://ftp.ncbi.nlm.nih.gov/genomes/genome_reports/) (Appendix 2) and the complete set of NCBI viral genomes (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/) (Appendix 3).

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BaseSpace was chosen as an appropriate release platform because while the entire set of software and dependencies can be deployed by the user from within a graphical user interface, the actual computation takes place in a controlled ‘cloud’ environment. Such a distribution strategy obviates the need to satisfy the multiple software or OS dependencies that often arises with academic computational methods. Results for SIANN are compiled into a report format, showing both the organisms that surpass 95% confidence, as well as the closest strain match for each species. The default view masks the raw data output, so that the results are human-readable and do not present extraneous information. While the code for execution and database- construction on a users system is available from Signature Science, LLC, additional databases on the BaseSpace platform can be made available upon request.

There is a neverending list of questions that one could ask of metagenomic sequencing data generated from important samples. Instead of answering them all, we demonstrate a technique with a very narrow focus that is able to report with a high degree of confidence whether a given set of organisms is present in a sample. These results are presented to the user in a comprehensible format, and accessible on a commonly-used web platform. The world of bioinformatics will continue to progress and develop more sophisticated tools for metagenomic analysis, and we hope that the utility of SIANN will convince others to package and benchmark their tools in a way that they can be used with confidence by the larger public, as well as the research community.

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Appendices

Appendix 1: Target Pathogen Database Arenaviridae Arenavirus Bacillus cytotoxicus NVH 391- Bunyaviridae Phlebovirus Rift- Golden-Gate-virus 98 Valley-fever-virus Arenaviridae Arenavirus Lujo- Bacillus mycoides DSM 2048 Burkholderia cenocepacia virus Bacillus mycoides Rock1-4 HI2424 Arenaviridae Flexal-virus Bacillus thuringiensis BMB171 Burkholderia cenocepacia segment-L Bacillus thuringiensis Bt407 J2315 Arenaviridae New-world- Bacillus thuringiensis HD-771 Burkholderia cenocepacia arenaviruses Allpahuayo-virus Bacillus thuringiensis serovar MC0-3 Arenaviridae New-world- chinensis CT-43 Burkholderia cepacia GG4 arenaviruses Chapare-virus Bacillus thuringiensis serovar Burkholderia gladioli BSR3 Arenaviridae New-world- konkukian 97-27 Burkholderia glumae BGR1 arenaviruses Guanarito-virus Brucella abortus A13334 Burkholderia mallei Arenaviridae New-world- Brucella ceti B1 94 2002721280 arenaviruses Junin-virus Brucella ceti M13 05 1 Burkholderia mallei ATCC Arenaviridae New-world- supercont1 22 10399 arenaviruses Machupo-virus Brucella melitensis ATCC Burkholderia mallei NCTC Arenaviridae New-world- 23457 10247 arenaviruses Sabia-virus Brucella melitensis bv 1 str 16M Burkholderia mallei SAVP1 Arenaviridae New-world- Brucella ovis ATCC 25840 Burkholderia multivorans arenaviruses Tacaribe-virus Brucella suis 1330 ATCC 17616 Arenaviridae New-world- Brucella suis ATCC 23445 Burkholderia oklahomensis arenaviruses Whitewater- Bunyaviridae Akabane-virus C6786 Arroyo-virus segment-M Burkholderia oklahomensis Arenaviridae Old-world- Bunyaviridae Hantavirus EO147 arenaviruses Ippy-virus Andes-virus Burkholderia pseudomallei Arenaviridae Old-world- Bunyaviridae Hantavirus 1026b arenaviruses Lassa-virus Dobrava-Belgrade-virus-strain- Burkholderia pseudomallei Arenaviridae Old-world- DOBV-Ano-Poroia-Afl9-1999 1106a arenaviruses Mopeia-virus- Bunyaviridae Hantavirus Burkholderia pseudomallei AN20410 Hantaan-virus 1710b Asfarviridae African-swine- Bunyaviridae Hantavirus Burkholderia pseudomallei fever-virus Benin-971- Puumala-virus 668 pathogenic-isolate Bunyaviridae Hantavirus Burkholderia pseudomallei Asfarviridae African-Swine- Seoul-virus-strain-Seoul-80-39- BPC006 Fever-Virus clone-1 Burkholderia pseudomallei Bacillus anthracis A2012 Bant Bunyaviridae Hantavirus Sin- K96243 02 1 Nombre-virus Burkholderia pyrrocinia CH-67 Bacillus anthracis Ames Bunyaviridae Hantavirus Burkholderia thailandensis Ancestor Thottapalayam-virus ATCC 700388 Bacillus anthracis Sterne Bunyaviridae Hantavirus Tula- Burkholderia thailandensis Bacillus cereus 03BB102 virus E264 Bacillus cereus AH187 Bunyaviridae Nairovirus Burkholderia thailandensis Bacillus cereus AH820 Crimean-Congo- MSMB121 Bacillus cereus ATCC 14579 hemorrhagic-fever-virus Campylobacter coli JV20 Bacillus cereus B4264 Bunyaviridae Nairovirus Campylobacter fetus subsp Bacillus cereus F65185 Dugbe-virus fetus 82-40 Campylobacter jejuni RM1221

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Campylobacter jejuni subsp Coccidioides posadasii CPA Coxiella burnetii Dugway doylei 26997 0020 5J108 111 Campylobacter jejuni subsp Coronaviridae Coxiella burnetii RSA 493 jejuni 81-176 Alphacoronavirus Bat- Diplorickettsia massiliensis 20B Campylobacter jejuni subsp coronavirus-HKU2 CS 1 jejuni NCTC 11168 ATCC Coronaviridae Ehrlichia canis str Jake 700819 Alphacoronavirus Feline- Ehrlichia chaffeensis str Campylobacter upsaliensis infectious-peritonitis-virus Arkansas JV21 Coronaviridae Ehrlichia chaffeensis str Clostridium acetobutylicum Alphacoronavirus Human- Sapulpa ctg90 DSM 1731 coronavirus-229E Ehrlichia ruminantium str Clostridium botulinum A str Coronaviridae Gardel ATCC 3502 Alphacoronavirus TGEV- Ehrlichia ruminantium str Clostridium botulinum Purdue-P115 Welgevonden BKT015925 Coronaviridae Bafinivirus Escherichia coli APEC O1 Clostridium botulinum B str White-bream-virus Escherichia coli BL21 DE3 Eklund 17B Coronaviridae Escherichia coli B str REL606 Clostridium botulinum E3 str Betacoronavirus Bovine- Escherichia coli ETEC H10407 Alaska E43 coronavirus Escherichia coli O104H4 str Clostridium botulinum F str Coronaviridae 2011C-3493 230613 Betacoronavirus Murine- Escherichia coli O157H7 str Clostridium botulinum H04402 hepatitis-virus-strain-A59 EC4115 065 Coronaviridae Escherichia coli O157H7 str Clostridium difficile 2007855 Betacoronavirus Murine- Sakai Clostridium difficile 630 hepatitis-virus-strain-JHM Escherichia coli O7K1 str CE10 Clostridium difficile BI1 Coronaviridae Escherichia coli O83H1 str Clostridium difficile BI9 Betacoronavirus SARS- NRG 857C Clostridium perfringens ATCC coronavirus Escherichia coli str K-12 substr 13124 Coronaviridae Coronavirinae MG1655 Clostridium perfringens SM101 Munia-coronavirus-HKU13- Filoviridae Ebolavirus Clostridium perfringens str 13 3514 Bundibugyo-ebolavirus Clostridium symbiosum WAL- Coronaviridae Filoviridae Ebolavirus Cote- 14163 Gammacoronavirus Avian- dIvoire-ebolavirus Clostridium symbiosum WAL- infectious-bronchitis-virus Filoviridae Ebolavirus Ebola- 14673 Coronaviridae virus-Mayinga-Zaire Clostridium tetani E88 Gammacoronavirus Turkey- Filoviridae Ebolavirus Reston- Clostridium thermocellum coronavirus ebolavirus ATCC 27405 Coronaviridae Torovirus Filoviridae Ebolavirus Sudan- Clostridium thermocellum Breda-virus ebolavirus DSM 1313 Coronaviridae unclassified- Filoviridae Marburgvirus Lake- Clostridium tunisiense TJ C661 coronaviruses Bat- Victoria-marburgvirus-Musoke Clostridium ultunense Esp coronavirus-BM48-31-BGR- Flaviviridae Alkhurma-virus Coccidioides immitis H5384 2008 Flaviviridae Classical-swine- Coccidioides immitis RMSCC Coronaviridae unclassified- fever-virus 2394 coronaviruses Bovine- Flaviviridae Dengue-virus 1 Coccidioides immitis RS respiratory-coronavirus-AH187 Flaviviridae Dengue-virus 2 Coccidioides posadasii C735 Coronaviridae unclassified- Flaviviridae Dengue-virus 3 delta SOWgp coronaviruses Human-enteric- Flaviviridae Dengue-virus 4 Coccidioides posadasii CPA coronavirus-strain-4408 Flaviviridae Japanese- 0001 Coxiella burnetii CbuG Q212 encephalitis-virus genome Flaviviridae Karshi-virus

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Flaviviridae Langat-virus Listeria monocytogenes FSL Poxviridae Lumpy-skin- Flaviviridae Louping-ill-virus R2-561 disease-virus NI-2490 Flaviviridae Murray-Valley- Listeria monocytogenes La111 Poxviridae Molluscipoxvirus encephalitis-virus Listeria seeligeri FSL N1-067 Molluscum-contagiosum-virus- Flaviviridae Omsk- Listeria seeligeri serovar 12b str subtype-1 hemorrhagic-fever-virus SLCC3954 Poxviridae Orthopoxvirus Flaviviridae Powassan-virus Listeria welshimeri serovar 6b Camelpox-virus Flaviviridae St-Louis- str SLCC5334 Poxviridae Orthopoxvirus encephalitis-virus Paramyxoviridae Avulavirus Cowpox-virus Flaviviridae Tick-borne- Newcastle-disease-virus-B1 Poxviridae Orthopoxvirus encephalitis-virus Paramyxoviridae Henipavirus Ectromelia-virus Flaviviridae Usutu-virus Hendra-virus Poxviridae Orthopoxvirus Flaviviridae West-Nile-virus Paramyxoviridae Henipavirus Monkeypox-virus-Zaire-96-I-16 Flaviviridae Yellow-fever-virus Nipah-virus Poxviridae Orthopoxvirus Francisella cf novicida Fx1 Paramyxoviridae Menangle- Taterapox-virus Francisella noatunensis subsp virus Poxviridae Orthopoxvirus orientalis str Toba 04 Paramyxoviridae Morbillivirus Vaccinia-virus Francisella novicida U112 Measles-virus Poxviridae Orthopoxvirus Francisella philomiragia subsp Paramyxoviridae Peste-des- Variola-virus philomiragia ATCC 25015 petits-ruminants-virus Poxviridae Sheeppox-virus Francisella philomiragia subsp Paramyxoviridae Respirovirus 17077-99 philomiragia ATCC 25017 Human-parainfluenza-virus-1 Poxviridae Suipoxvirus Francisella tularensis subsp Paramyxoviridae Respirovirus Swinepox-virus holarctica F92 Human-parainfluenza-virus-3 Puccinia graminis f sp tritici Francisella tularensis subsp Paramyxoviridae Respirovirus CRL 75-36-700-3 mediasiatica FSC147 Sendai-virus Ralstonia pickettii 12D Francisella tularensis subsp Paramyxoviridae Rinderpest- Ralstonia pickettii 12J tularensis FSC198 virus strain-Kabete-O Ralstonia solanacearum Herpesviridae Alcelaphine- Paramyxoviridae Rubulavirus CFBP2957 herpesvirus 1 Human-parainfluenza-virus-2 Ralstonia solanacearum Herpesviridae Macacine- Paramyxoviridae Rubulavirus CMR15 herpesvirus 1 Human-parainfluenza-virus-4a Ralstonia solanacearum Listeria fleischmannii LU2006-1 Paramyxoviridae Rubulavirus GMI1000 c88 Mumps-virus Rathayibacter toxicus DSM Listeria innocua Clip11262 Picornaviridae Foot-and- 7488 Listeria innocua FSL J1-023 mouth-disease-virus -type-O Reoviridae African- Listeria ivanovii FSL F6-596 Picornaviridae Swine- horsesickness-virus segment- Listeria ivanovii subsp ivanovii vesicular-disease-virus strain- 10 PAM 55 HK70 Rhabdoviridae Vesicular- Listeria marthii FSL S4-120 Picornaviridae Swine- stomatitis-Indiana-virus Listeria monocytogenes vesicular-disease-virus strain- Rhabdoviridae Vesicular- 07PF0776 NET192 stomatitis-virus strain- Listeria monocytogenes 08- Poxviridae Avipoxvirus NJ2075212NM 5578 Fowlpox-virus Rickettsia bellii OSU 85-389 Listeria monocytogenes Poxviridae Crocodylidpoxvirus Rickettsia conorii str Malish 7 10403S Nile-crocodilepox-virus Rickettsia prowazekii str Breinl Listeria monocytogenes ATCC Poxviridae Goatpox-virus Rickettsia prowazekii str 19117 Pellor RpGvF24 Listeria monocytogenes Poxviridae Leporipoxvirus Rickettsia rickettsii str Arizona Finland 1998 Myxoma-virus Rickettsia typhi str B9991CWPP Rickettsiella grylli gcontig 634

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Salmonella bongori N268-08 Staphylococcus capitis SK14 Xanthomonas oryzae pv Salmonella bongori NCTC Staphylococcus caprae C87 oryzae MAFF 311018 12419 Staphylococcus carnosus Xanthomonas oryzae pv Salmonella enterica subsp subsp carnosus TM300 oryzae PXO99A arizonae serovar 62z4z23- str Staphylococcus epidermidis Xanthomonas vasicola pv RSK2980 ATCC 12228 vasculorum NCPPB 1326 scf Salmonella enterica subsp Staphylococcus epidermidis 9767 4580 enterica serovar Dublin str CT RP62A Yersinia aldovae ATCC 35236 02021853 Staphylococcus equorum Yersinia bercovieri ATCC Salmonella enterica subsp subsp equorum Mu2 43970 enterica serovar Newport str Staphylococcus haemolyticus Yersinia enterocolitica IP SL254 JCSC1435 10393 Salmonella enterica subsp Staphylococcus hominis Yersinia enterocolitica IP2222 enterica serovar Paratyphi A SK119 Yersinia enterocolitica subsp str ATCC 9150 Staphylococcus hominis enterocolitica 8081 Salmonella enterica subsp subsp hominis C80 Yersinia enterocolitica subsp enterica serovar Typhimurium Staphylococcus lugdunensis palearctica 105 5R str LT2 HKU09-01 Yersinia frederiksenii ATCC Salmonella enterica subsp Staphylococcus lugdunensis 33641 enterica serovar Typhi str Ty2 N920143 Yersinia intermedia ATCC Shigella boydii CDC 3083-94 Togaviridae Alphavirus 29909 Shigella boydii Sb227 Barmah-Forest-virus Yersinia kristensenii ATCC Shigella dysenteriae Sd197 Togaviridae Chikungunya- 33638 Shigella flexneri 2002017 virus Yersinia mollaretii ATCC 43969 Shigella flexneri 2a str 2457T Togaviridae EEEV-complex Yersinia pestis A1122 Shigella flexneri 2a str 301 Eastern-equine-encephalitis- Yersinia pestis Antiqua Shigella flexneri 5 str 8401 virus Yersinia pestis KIM 10 Shigella sonnei 53G Togaviridae Rubivirus Rubella- Yersinia pestis Pestoides F Shigella sonnei Ss046 virus Yersinia pseudotuberculosis IP Staphylococcus arlettae Togaviridae SFV-complex O- 31758 CVD059 SARL c230 nyong-nyong-virus Yersinia pseudotuberculosis IP Staphylococcus aureus 04- Togaviridae Venezuelan- 32953 02981 equine-encephalitis-virus Yersinia pseudotuberculosis Staphylococcus aureus Togaviridae WEEV-complex PB1 08BA02176 Sindbis-virus Yersinia pseudotuberculosis Staphylococcus aureus subsp Togaviridae Western-equine- YPIII aureus N315 encephalomyelitis-virus Yersinia rohdei ATCC 43380 Staphylococcus aureus subsp Xanthomonas albilineans GPE Yersinia ruckeri ATCC 29473 aureus NCTC 8325 PC73 Staphylococcus aureus subsp Xanthomonas axonopodis aureus TW20 Xac29-1 Staphylococcus capitis QN1 Xanthomonas oryzae pv Contig63 oryzae KACC 10331

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Appendix 2: Viral Database Abaca bunchy top virus DNA- Adoxophyes orana Alternanthera yellow vein C granulovirus virus satellite DNA beta Abaca bunchy top virus DNA- Adoxophyes orana Ambystoma tigrinum virus M nucleopolyhedrovirus Amsacta moorei Abaca bunchy top virus DNA- Aedes aegypti densovirus entomopoxvirus L N Aedes albopictus densovirus Anguillid herpesvirus 1 Abaca bunchy top virus DNA- Aedes taeniorhynchus Anopheles gambiae R iridescent virus densonucleosis virus Abaca bunchy top virus DNA- Aeromonas phage 25 Antheraea pernyi S Aeromonas phage 31 nucleopolyhedrovirus Abaca bunchy top virus Aeromonas phage 44RR2.8t Anticarsia gemmatalis segment 2 Aeromonas phage Aeh1 nucleopolyhedrovirus Abalone shriveling syndrome- Aeromonas phage phiO18P Archaeal BJ1 virus associated virus african cassava mosaic virus Ateline herpesvirus 3 Abutilon Brazil virus DNA A DNA A Autographa californica Abutilon Brazil virus DNA B african cassava mosaic virus nucleopolyhedrovirus Abutilon mosaic virus DNA A DNA B Avian adeno-associated virus Abutilon mosaic virus DNA B African green monkey ATCC VR-865 Acanthocystis turfacea polyomavirus Avian adeno-associated virus Chlorella virus 1 African swine fever virus strain DA-1 Acheta domesticus Ageratum enation virus Avian endogenous retrovirus densovirus Ageratum leaf Cameroon EAV-HP Acholeplasma phage L2 betasatellite Azospirillum phage Cd Acholeplasma phage MV-L1 Ageratum leaf curl virus-G52 Bacillus phage 0305phi8-36 Acidianus bottle-shaped virus Ageratum yellow vein China Bacillus phage AP50 Acidianus filamentous virus 1 virus-associated DNA beta Bacillus phage B103 Acidianus filamentous virus 2 Ageratum yellow vein Bacillus phage Bam35c Acidianus filamentous virus 3 Chinavirus Bacillus phage BCJA1c Acidianus filamentous virus 6 Ageratum yellow vein Hualian Bacillus phage Cherry Acidianus filamentous virus 7 virus-TaiwanHsinchutom2003 Bacillus phage Fah Acidianus filamentous virus 8 DNA A Bacillus phage GA-1 Acidianus filamentous virus 9 Ageratum yellow vein Sri Bacillus phage Gamma Acidianus rod-shaped virus 1 Lanka virus segment A Bacillus phage GIL16c Acidianus spindle-shaped Ageratum yellow vein Taiwan Bacillus phage IEBH virus 1 virus Bacillus phage phi105 Acidianus two-tailed virus Ageratum yellow vein Bacillus phage phi29 Actinomyces phage Av-1 virusassociated DNA beta Bacillus phage SPBc2 Actinoplanes phage phiAsp2 Ageratum yellow veinvirus Bacillus phage SPO1 Acyrthosiphon pisum Agrotis ipsilon multiple Bacillus phage SPP1 bacteriophage APSE-1 nucleopolyhedrovirus Bacillus phage TP21-L Adeno-associated virus-1 Agrotis segetum granulovirus Bacillus phage WBeta Adeno-associated virus-2 Agrotis segetum Bacillus prophage phBC6A51 Adeno-associated virus-3 nucleopolyhedrovirus Bacillus prophage phBC6A52 Adeno-associated virus-4 Alcelaphine herpesvirus 1 Bacillus virus 1 Adeno-associated virus 5 Aleutian mink disease virus Bacteriophage Aaphi23 Adeno-associated virus-7 Allamanda leaf curl virus Bacteriophage APSE-2 Adeno-associated virus-8 DNA-A Bacteriophage PSA Adoxophyes honmai NPV Alternanthera yellow vein Bacteriophage RB32 virus DNA-A Bacteroides phage B40-8

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Banana bunchy top virus DNA Begomovirus-associated DNA Burkholderia ambifaria phage C II BcepF1 Banana bunchy top virus DNA Begomovirus-associated Burkholderia phage Bcep 176 M DNA-III Burkholderia phage Bcep1 Banana bunchy top virus DNA Bettongia penicillata Burkholderia phage Bcep22 N papillomavirus 1 Burkholderia phage Bcep43 Banana bunchy top virus DNA Bhendi yellow vein Burkholderia phage Bcep781 R Bhubhaneswar virus DNA-A Burkholderia phage BcepB1A Banana bunchy top virus DNA Bhendi yellow vein Delhi virus Burkholderia phage BcepC6B S 2004New Delhi DNA-A Burkholderia phage Banana bunchy top virus DNA Bhendi yellow vein mosaic BcepGomr U3 virus-associated DNA beta Burkholderia phage BcepIL02 Banana streak GF virus Bhendi yellow vein mosaic Burkholderia phage BcepMu Banana streak Mysore virus Virus Burkholderia phage Banana streak OL virus Bitter gourd leaf curl disease- BcepNazgul Banana streak virus genome associated DNA beta Burkholderia phage BcepNY3 Banana streak virus strain BK polyomavirus Burkholderia phage KS10 Acuminata Vietnam Blainvillea yellow spot virus Burkholderia phage KS9 Bandicoot papillomatosis DNA-A Burkholderia phage phi1026b carcinomatosis virus type 1 Blainvillea yellow spot virus Burkholderia phage phi644-2 Bandicoot papillomatosis DNA-B chromosome carcinomatosis virus type 2 Blattella germanica Burkholderia phage phiE12-2 Bat adeno-associated virus densovirus chromosome YNM Blueberry red ringspot virus Burkholderia phage phiE125 Bdellovibrio phage phiMH2K Bocavirus gorillaGBoV12009 Burkholderia phage phiE202 Beak and feather disease Bombyx mandarina chromosome virus nucleopolyhedrovirus Burkholderia phage phiE255 Bean calico mosaic virus DNA Bombyx mori densovirus 5 chromosomeBurkholderia A Bombyx mori NPV prophage phi52237 Bean calico mosaic virus DNA Bordetella phage BIP-1 Cabbage leaf curl virus DNA B Bordetella phage BMP-1 A Bean dwarf mosaic virus DNA Bordetella phage BPP-1 Cabbage leaf curl virus DNA A Bougainvillea spectabilis B Bean dwarf mosaic virus DNA chlorotic vein-banding virus Cacao swollen shoot virus B Bovine adeno-associated California sea lion anellovirus Bean golden mosaic virus virus California sea lion DNA A Bovine adenovirus A polyomavirus 1 Bean golden mosaic virus Bovine adenovirus B Callitrichine herpesvirus 3 DNA B Bovine adenovirus D strain CJ0149 Bean golden yellow mosaic Bovine ephemeral fever virus Camelpox virus virus DNA A Bovine foamy virus Campoletis sonorensis Bean golden yellow mosaic Bovine herpesvirus 1 ichnovirus chromosome virus DNA B Bovine herpesvirus 4 long segment W Bean yellow dwarf virus unique region Campoletis sonorensis putative genes V1 Bovine herpesvirus 5 ichnovirus segment B Beet curly top Iran virus-K Bovine papillomavirus-1 Campoletis sonorensis Beet curly top virus-California Bovine papillomavirus 3 ichnovirus segment C Logan Bovine papular stomatitis virus Campoletis sonorensis Beet mild curly top virus- Bovine parvovirus 2 ichnovirus segment D Worland4 Bovine Parvovirus Campoletis sonorensis Beet severe curly top virus-Cfh Bovine polyomavirus ichnovirus segment E

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Campoletis sonorensis Capra hircus papillomavirus Circovirus-like genome RW-E ichnovirus segment F type 1 Circovirus-like genome SAR-A Campoletis sonorensis Cardiospermum yellow leaf Circovirus-like genome SAR-B ichnovirus segmentG2 curl virus satellite DNA beta Citrus psorosis virus RNA1 Campoletis sonorensis Caretta caretta Citrus psorosis virus RNA2 ichnovirus segment G papillomavirus 1 Citrus psorosis virus RNA3 Campoletis sonorensis Carnation etched ring virus Citrus yellow mosaic virus ichnovirus segment H Casphalia extranea Clanis bilineata Campoletis sonorensis densovirus nucleopolyhedrosis virus ichnovirus segmentI2 Cassava vein mosaic virus Clavibacter phage CMP1 Campoletis sonorensis Cauliflower mosaic virus Clerodendron yellow mosaic ichnovirus segment I Cercopithecine herpesvirus 2 virus Campoletis sonorensis Cercopithecine herpesvirus 5 Clerodendrum golden mosaic ichnovirus segment J strain 2715 China virus DNA A Campoletis sonorensis Cercopithecine herpesvirus 9 Clerodendrum golden mosaic ichnovirus segment L Cestrum yellow leaf curling China virus DNA B Campoletis sonorensis virus Clerodendrum golden mosaic ichnovirus segment M Chaetoceros salsugineum virus DNA-A Campoletis sonorensis DNA virus Clerodendrum golden mosaic ichnovirus segment N Chayote yellow mosaic virus virus DNA-B Campoletis sonorensis Chicken anemia virus Clostridium phage 39-O ichnovirus segment O1 Chickpea chlorotic dwarf Clostridium phage c-st Campoletis sonorensis virus Clostridium phage phi3626 ichnovirus segment P Chilli leaf curl disease Clostridium phage phiC2 Campoletis sonorensis associated sequence virion Clostridium phage phi CD119 ichnovirus segment Q Chilli leaf curl Multan Clostridium phage phiCD27 Campoletis sonorensis alphasatellite Clostridium phage phiCTP1 ichnovirus segment T Chilli leaf curl virus Coconut foliar decay virus Campoletis sonorensis Chino del tomate virus DNA A Columbid circovirus ichnovirus segment U Chino del tomate virus DNA B Commelina yellow mottle Campoletis sonorensis Chlamydia phage 3 virus ichnovirus segment V Chlamydia phage 4 Corchorus golden mosaic Campoletis sonorensis Chlamydia phage Chp1 virus DNA-A ichnovirus segment Z Chlamydia phage Chp2 Corchorus golden mosaic Campoletis sonorensis Chlamydia phage PhiCPG1 virus DNA-B ichnovirus superhelical Chloris striate mosaic virus Corchorus yellow spot virus segment A Choristoneura fumiferana DEF DNA A Campoletis sonorensis MNPV Corchorus yellow spot virus ichnovirus superhelical Choristoneura fumiferana DNA B segment aprime MNPV Corchorus yellow vein virus- Canary circovirus Choristoneura occidentalis Hoa Binh DNA A Canarypox virus granulovirus Corchorus yellow vein virus- Canine adenovirus Chrysodeixis chalcites Hoa Binh DNA B Canine minute virus nucleopolyhedrovirus Corynebacterium phage Canine oral papillomavirus Circovirus-like genome BBC-A BFK20 Canine papillomavirus 2 Circovirus-like genome CB-A Corynebacterium phage Canine papillomavirus 3 Circovirus-like genome CB-B P1201 Canine papillomavirus 4 Circovirus-like genome RW-A Cotesia congregata Canine papillomavirus 6 Circovirus-like genome RW-B bracovirus segment Circle10 Canine parvovirus Circovirus-like genome RW-C Cotesia congregata Circovirus-like genome RW-D bracovirus segment Circle11

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Cotesia congregata Cotesia congregata virus Croton yellow vein virus bracovirus segment Circle12 segment Circle6 Crow polyomavirus Cotesia congregata Cotesia congregata virus Cryptophlebia leucotreta bracovirus segment Circle13 segment Circle7 granulovirus Cotesia congregata Cotesia congregata virus Cucurbita yellow vein virus- bracovirus segment Circle14 segment Circle8 associated DNA beta Cotesia congregata Cotton leaf crumple Cucurbit leaf crumple virus bracovirus segment Circle15 geminivirus DNA B DNA A Cotesia congregata Cotton leaf crumple virus DNA Cucurbit leaf crumple virus bracovirus segment Circle17 A DNA B Cotesia congregata Cotton leaf curl Alabad virus Culex nigripalpus NPV bracovirus segment Circle19 Cotton leaf curl Bangalore Culex pipiens densovirus Cotesia congregata virus-associated DNA beta Cyanophage PSS2 bracovirus segment circle1 Cotton leaf curl Bangalore Cyanophage Syn5 Cotesia congregata virus segment A Cycad leaf necrosis virus bracovirus segment Circle20 Cotton leaf curl Burewala Cydia pomonella granulovirus Cotesia congregata alphasatellite Cyprinid herpesvirus 3 bracovirus segment Circle21 Cotton leaf curl Burewala Deer papillomavirus Cotesia congregata betasatellite Deerpox virus W-1170-84 bracovirus segment Circle22 Cotton leaf curl Burewala Deerpox virus W-848-83 Cotesia congregata virus-IndiaVehari2004 Deftia phage phiW-14 bracovirus segment Circle23 Cotton leaf curl Gezira Dendrolimus punctatus Cotesia congregata alphasatellite densovirus bracovirus segment Circle25 Cotton leaf curl Gezira beta Desmodium leaf distortion Cotesia congregata Cotton leaf curl Gezira virus DNA A bracovirus segment Circle26 Betasatellite Desmodium leaf distortion Cotesia congregata extrachromosomal virus DNA B bracovirus segment circle2 Cotton leaf curl Gezira virus Diadromus pulchellus Cotesia congregata Cotton leaf curl Kokhran virus ascovirus 4a bracovirus segment Circle30 Cotton leaf curl Multan Virus Diatraea saccharalis Cotesia congregata Cotton leaf curl Multan virus densovirus bracovirus segment Circle31 satellite DNA beta Dicliptera yellow mottle virus Cotesia congregata Cotton leaf curl Multan virus DNA A bracovirus segment Circle32 satellite U36-1 Dicliptera yellow mottle virus Cotesia congregata Cotton leaf curl Rajasthan DNA B bracovirus segment Circle33 virus segment A Digitaria streak virus Cotesia congregata Cotton leaf curl virus- Dioscorea bacilliform virus bracovirus segment Circle35 associated DNA beta Dolichos yellow mosaic virus Cotesia congregata Cottontail rabbit Dracaena mottle virus bracovirus segment Circle36 papillomavirus Duck adenovirus A Cotesia congregata Cowpea severe leaf curl- Duck circovirus bracovirus segment circle3 associated DNA beta Duck hepatitis B virus Cotesia congregata Cowpox virus East African cassava mosaic bracovirus segment Circle4 Crassocephalum yellow vein Cameroon virus DNA A Cotesia congregata virus-Jinghong East African cassava mosaic bracovirus segment Circle5 Croton yellow vein mosaic Cameroon virus DNA B Cotesia congregata alphasatellite East African cassava mosaic bracovirus segment Circle9 Croton yellow vein mosaic Kenya virus DNA A Cotesia congregata virus virus East African cassava mosaic segment Circle18 Croton yellow vein mosaic Kenya virus DNA B Virus satellite DNA beta

21 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

East African cassava mosaic Enterobacteria phage Min27 Enterococcus faecalis 62 virus DNA A Enterobacteria phage Mu plasmid EF62pB East African cassava mosaic Enterobacteria phage N15 Enterococcus faecalis 62 virus DNA B Enterobacteria phage N4 plasmid EF62pC East African cassava mosaic Enterobacteria phage P1 Enterococcus phage EF62phi Zanzibar virus DNA-A Enterobacteria phage P22 Enterococcus phage EFAP-1 East African cassava mosaic virus Enterococcus phage phiEf11 Zanzibar virus DNA B Enterobacteria phage P2 virus Enterococcus phage Ecotropis obliqua NPV Enterobacteria phage P4 phiEF24C Ectocarpus siliculosus virus 1 Enterobacteria phage Phi1 Enterococcus phage phiFL1A Ectromelia virus Enterobacteria phage Enterococcus phage phiFL2A Emiliania huxleyi virus 86 phiEco32 Enterococcus phage phiFL3A Emilia yellow vein virus- Enterobacteria phage Enterococcus phage phiFL4A associated DNA beta phiEcoM-GJ1 Enzootic nasal tumour virus of Emilia yellow vein virus-Fz1 Enterobacteria phage phiP27 goats Enterobacteria phage 13a Enterobacteria phage Epiphyas postvittana NPV Enterobacteria phage 933W phiX174 sensu lato Equid herpesvirus 1 Enterobacteria phage alpha3 Enterobacteria phage PRD1 Equid herpesvirus 2 Enterobacteria phage BA14 Enterobacteria phage PsP3 Equid herpesvirus 4 Enterobacteria phage BP- Enterobacteria phage RB14 Equid herpesvirus 9 4795 Enterobacteria phage RB16 Equine papillomavirus 2 Enterobacteria phage Enterobacteria phage RB43 Eragrostis curvula streak virus EcoDS1 Enterobacteria phage RB49 Eragrostis streak virus Enterobacteria phage EPS7 Enterobacteria phage RB51 Erectites yellow mosaic virus Enterobacteria phage Enterobacteria phage RB69 DNA-A epsilon15 Enterobacteria phage RTP Erectites yellow mosaic virus Enterobacteria phage ES18 Enterobacteria phage Sf6 satellite DNA beta Enterobacteria phage Felix 01 Enterobacteria phage SfV Erethizon dorsatum Enterobacteria phage Fels-2 Enterobacteria phage SP6 papillomavirus type 1 Enterobacteria phage G4 Enterobacteria phage SSL- Erinaceus europaeus Enterobacteria phage HK022 2009a papillomavirus Enterobacteria phage HK620 Enterobacteria phage ST104 Erwinia amylovora phage Enterobacteria phage HK97 Enterobacteria phage St-1 Era103 Enterobacteria phage I2-2 Enterobacteria phage ST64T Erwinia phage phiEa21-4 Enterobacteria phage ID18 Enterobacteria phage T1 Escherichia coli Enterobacteria phage ID2 Enterobacteria phage T3 bacteriophage rv5 MoscowID2001 Enterobacteria phage T4 Escherichia phage D108 Enterobacteria phage If1 Enterobacteria phage T5 Escherichia phage phiV10 Enterobacteria phage Ike Enterobacteria phage T7 Eupatorium vein clearing virus Enterobacteria phage IME08 Enterobacteria phage TLS Eupatorium yellow vein Enterobacteria phage JK06 Enterobacteria phage VT2- associated DNA beta Enterobacteria phage JS10 Sakai Eupatorium yellow vein virus Enterobacteria phage JS98 Enterobacteria phage WA13 Euphorbia leaf curl virus DNA Enterobacteria phage JSE Enterobacteria phage WV8 A Enterobacteria phage K1-5 Enterobacteria phage YYZ- Euphorbia yellow mosaic virus Enterobacteria phage K1E 2008 DNA A Enterobacteria phage K1F Enterococcus faecalis 62 Euphorbia yellow mosaic virus Enterobacteria phage chromosome DNA B lambda Enterococcus faecalis 62 Euproctis pseudoconspersa Enterobacteria phage LKA1 plasmid EF62pA nucleopolyhedrovirus Enterobacteria phage M13 European elk papillomavirus

22 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Faba bean necrotic stunt virus Frog adenovirus 1 Glypta fumiferanae ichnovirus DNA C Frog virus 3 segment B19 Faba bean necrotic stunt virus Galleria mellonella densovirus Glypta fumiferanae ichnovirus DNA M Gallid herpesvirus 1 segment-B1 Faba bean necrotic stunt virus Gallid herpesvirus 2 Glypta fumiferanae ichnovirus DNA N Gallid herpesvirus 3 segment B20 Faba bean necrotic stunt virus Gammapapillomavirus Glypta fumiferanae ichnovirus DNA R HPV127 segment B21 Faba bean necrotic stunt virus Geobacillus phage GBSV1 Glypta fumiferanae ichnovirus DNA S Geobacillus virus E2 segment B22 Faba bean necrotic stunt virus Glossina pallidipes salivary Glypta fumiferanae ichnovirus DNA U1 gland hypertrophy virus segment B23 Faba bean necrotic stunt virus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus DNA U2 segmentA10 segment B24 Faba bean necrotic stunt virus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus DNA U4 segment A1 segment B25 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 10 segment A2 segment B26 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA-1 segment A3 segment B27 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 2 segment A4 segment B28 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 4 segment A5 segment B29 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 5 segment A6 segment-B2 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 7 segment A7 segment B30 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 8 segment A8 segment B31 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus virus DNA 9 segment A9 segment B32 Faba bean necrotic yellows Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Virus segment B10 segment B33 Feldmannia species virus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Felid herpesvirus 1 segment B11 segment B34 Felis domesticus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus papillomavirus type 1 segment B12 segment B35 Fenneropenaeus chinensis Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus hepatopancreatic densovirus segment B13 segment B36 Figwort mosaic virus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Finch circovirus segment B14 segment B37 Finch polyomavirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Flavobacterium phage 11b segment B15 segment B38 Fowl adenovirus A Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Fowl adenovirus D segment B16 segment B39 Fowlpox virus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Francolinus leucoscepus segment B17 segment-B3 papillomavirus 1 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Fringilla coelebs segment B18 segment B40 papillomavirus

23 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B41 segment B64 segment C7 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B42 segment B65 segment C8 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B43 segment-B6 segment C9 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B44 segment B7 segment D1 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B45 segment B8 segment D2 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B46 segment B9 segment D3 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B47 segment C10 segment D4 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B48 segment C11 segment D5 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B49 segment C12 segment D6 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment-B4 segment C13 segment D7 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus segment B50 segment C14 segment E1 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Goatpox virus Pellor segment B51 segment C15 Goose circovirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Goose hemorrhagic segment B52 segment C16 polyomavirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Goose parvovirus segment B53 segment C17 Gossypium darwinii Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus symptomless alphasatellite segment B54 segment C18 DNA-alpha Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Gossypium darwinii segment B55 segment C19 symptomless virus DNA-A Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Gossypium davidsonii segment B56 segment-C1 symptomless alphasatellite Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus DNA-alpha-B segment B57 segment C20 Gossypium mustilinum Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus symptomless alphasatellite segment B58 segment C21 DNA-alpha-B Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Gossypium punctatum mild segment B59 segment C22 leaf curl virus DNA A Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Gossypium punctatum mild segment-B5 segment-C2 leaf curl virus DNA B Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Ground squirrel hepatitis virus segment B60 segment C3 Gryllus bimaculatus nudivirus Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Gull circovirus segment B61 segment C4 Haemophilus phage HP1 Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus Haemophilus phage HP2 segment B62 segment C5 Haloarcula hispanica Glypta fumiferanae ichnovirus Glypta fumiferanae ichnovirus pleomorphic virus 1 segment B63 segment C6 Haloarcula phage SH1 Halomonas phage phiHAP-1

24 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Halorubrum phage HF2 Human adenovirus F Hyperthermophilic Archaeal Halorubrum pleomorphic virus Human bocavirus 1 Virus 1 1 Human bocavirus 2 Hyperthermophilic Archaeal Halovirus HF1 Human bocavirus 3 Virus 2 Hamster polyomavirus Human bocavirus 4 Hyphantria cunea Helicoverpa armigera Human erythrovirus V9 nucleopolyhedrovirus granulovirus Human herpesvirus 1 Hyposoter fugitivus ichnovirus Helicoverpa armigera Human herpesvirus 2 segment A1 multiple nucleopolyhedrovirus Human herpesvirus 3 Hyposoter fugitivus ichnovirus Helicoverpa armigera-NPV Human herpesvirus 4 segment A2 Helicoverpa armigera NPV Human herpesvirus 5 strain Hyposoter fugitivus ichnovirus NNg1 Merlin segment A3 Helicoverpa armigera Human herpesvirus 7 Hyposoter fugitivus ichnovirus nucleopolyhedrovirus G4 Human herpesvirus 8 segment B10 Helicoverpa zea SNPV Human papillomavirus-18 Hyposoter fugitivus ichnovirus Heliothis virescens ascovirus Human papillomavirus 1 segment B11 3e Human papillomavirus-2 Hyposoter fugitivus ichnovirus Hepatitis B virus Human papillomavirus 54 segment B12 Heron hepatitis B virus Human papillomavirus-5 Hyposoter fugitivus ichnovirus His1 virus Human papillomavirus type segment B13 His2 virus 101 Hyposoter fugitivus ichnovirus Hollyhock leaf crumple virus Human papillomavirus type segment B14 Honeysuckle yellow vein 103 Hyposoter fugitivus ichnovirus beta-JapanFukui2001 Human papillomavirus type segment B15 Honeysuckle yellow vein 108 Hyposoter fugitivus ichnovirus mosaic beta- Human papillomavirus type- segment B16 JapanMiyizaki2001 10 Hyposoter fugitivus ichnovirus Honeysuckle yellow vein Human papillomavirus type 16 segment B17 mosaic disease associated Human papillomavirus type 26 Hyposoter fugitivus ichnovirus satellite DNA beta-Ibaraki Human papillomavirus type 32 segment B18 Honeysuckle yellow vein Human papillomavirus type 34 Hyposoter fugitivus ichnovirus mosaic Virus Human papillomavirus type 41 segment-B1 Honeysuckle yellow vein Human papillomavirus type 48 Hyposoter fugitivus ichnovirus mosaic virus-Kagoshima Human papillomavirus type 49 segment B2 Honeysuckle yellow vein Human papillomavirus type-4 Hyposoter fugitivus ichnovirus mosaic virus satellite DNA Human papillomavirus type 50 segment B3 beta Human papillomavirus type 53 Hyposoter fugitivus ichnovirus Honeysuckle yellow vein virus- Human papillomavirus type 60 segment B4 UK1 Human papillomavirus type 63 Hyposoter fugitivus ichnovirus Horsegram yellow mosaic Human papillomavirus type segment B5 Virus DNA B 6b Hyposoter fugitivus ichnovirus Horsegram yellow mosaic Human papillomavirus type 7 segment B6 virus Human papillomavirus type 88 Hyposoter fugitivus ichnovirus Horseradish curly top virus Human papillomavirus type 90 segment B7 Human adenovirus 54 Human papillomavirus type 92 Hyposoter fugitivus ichnovirus Human adenovirus AHuman Human papillomavirus type 96 segment B8 adenovirus B1 Human papillomavirus type-9 Hyposoter fugitivus ichnovirus Human adenovirus B2 Human parvovirus B19 segment B9 Human adenovirus C Human T-lymphotropic virus 1 Hyposoter fugitivus ichnovirus Human adenovirus D Human T-lymphotropic virus 4 segment C10 Human adenovirus E

25 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus phage Lc-Nu segment C11 segment D4 Lactobacillus phage LL-H Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus phage LP65 segment C12 segment D5 Lactobacillus phage Lrm1 Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus phage Lv-1 segment C13 segment D6 Lactobacillus phage phiAT3 Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus phage phig1e segment C14 segment D7 Lactobacillus phage phiJL-1 Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus prophage Lj928 segment C15 segment D8 Lactobacillus prophage Lj965 Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactobacillus prophage segment C16 segment D9 phiadh Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactococcus phage 1706 segment C17 segment E1 Lactococcus phage 4268 Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus Lactococcus phage 712 segment C18 segment E2 Lactococcus phage Hyposoter fugitivus ichnovirus Hyposoter fugitivus ichnovirus asccphi28 segment C19 segment G1 Lactococcus phage bIBB29 Hyposoter fugitivus ichnovirus Ictalurid herpesvirus 1 strain Lactococcus phage bIL170 segment-C1 Auburn 1 Lactococcus phage bIL67 Hyposoter fugitivus ichnovirus Indian cassava mosaic virus Lactococcus phage BK5-T segment C20 DNA A Lactococcus phage c2 Hyposoter fugitivus ichnovirus Indian cassava mosaic virus Lactococcus phage jj50 segment-C2 DNA B Lactococcus phage KSY1 Hyposoter fugitivus ichnovirus Infectious hypodermal and Lactococcus phage P008 segment C3 hematopoietic necrosis virus Lactococcus phage P087 Hyposoter fugitivus ichnovirus Infectious spleen and kidney Lactococcus phage phiLC3 segment C4 necrosis virus Lactococcus phage Q54 Hyposoter fugitivus ichnovirus Invertebrate iridescent virus 6 Lactococcus phage r1t segment C5 Iodobacteriophage phiPLPE Lactococcus phage sk1 Hyposoter fugitivus ichnovirus Ipomoea yellow vein virus Lactococcus phage TP901-1 segment C6 Jatropha leaf curl virus DNA A Lactococcus phage Tuc2009 Hyposoter fugitivus ichnovirus Jatropha yellow mosaic India Lactococcus phage ul36 segment C7 virus DNA-A Lactococcus prophage Hyposoter fugitivus ichnovirus JC polyomavirus bIL285 segment C8 Junonia coenia densovirus Lactococcus prophage Hyposoter fugitivus ichnovirus Kalanchoe top-spotting virus bIL286 segment C9 Kenaf leaf curl virus DNA A Lactococcus prophage Hyposoter fugitivus ichnovirus KI polyomavirus Stockholm 60 bIL309 segment D10 Klebsiella phage KP15 Lactococcus prophage Hyposoter fugitivus ichnovirus Klebsiella phage KP32 bIL310 segment D11 Klebsiella phage KP34 Lactococcus prophage Hyposoter fugitivus ichnovirus Klebsiella phage phiKO2 bIL311 segment D12 Kluyvera phage Kvp1 Lactococcus prophage Hyposoter fugitivus ichnovirus Kudzu mosaic virus DNA-A bIL312 segment-D1 Kudzu mosaic virus DNA-B Lamium leaf distortion Hyposoter fugitivus ichnovirus Lactobacillus johnsonii associated virus segment D2 prophage Lj771 Leucania separata nuclear Hyposoter fugitivus ichnovirus Lactobacillus phage A2 polyhedrosis virus segment D3 Lactobacillus phage KC5a Leucas zeylanica yellow vein Lactobacillus phage Lb338-1 virus satellite DNA beta

26 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Lindernia anagallis yellow vein JamaicaWissadulaAugust Mastomys natalensis virus DNA-A Town DNA B papillomavirus Lindernia anagallis yellow vein Macroptilium mosaic Puerto Melanoplus sanguinipes virus satellite DNA beta Rico virus DNA A entomopoxvirus Listeria phage A006 Macroptilium mosaic Puerto Meleagrid herpesvirus 1 Listeria phage A118 Rico virus DNA B Melon chlorotic leaf curl virus Listeria phage A500 Macroptilium yellow mosaic DNA A Listeria phage A511 Florida virus DNA A Melon chlorotic mosaic virus- Listeria phage B025 Macroptilium yellow mosaic associated alphasatellite Listeria phage B054 Florida virus DNA B Melon chlorotic mosaic virus Listeria phage P35 Macroptilium yellow mosaic DNA-A Listeria phage P40 virus DNA A Melon chlorotic mosaic virus Listonella phage phiHSIC Macroptilium yellow mosaic DNA-B Loofa yellow mosaic virus virus DNA B Merkel cell polyomavirus DNA A Maize streak virus-ASouth Merremia mosaic virus DNA A Loofa yellow mosaic virus Africa Merremia mosaic virus DNA B DNA B Malachra yellow vein mosaic Mesta yellow vein mosaic Lucky bamboo bacilliform virus-associated satellite DNA Bahraich virus- virus beta IndiaBahraich2007 DNA A Ludwigia leaf distortion Mal de Rio Cuarto virus Mesta yellow vein mosaic betasatellite segment 9 virus-associated DNA beta IndiaAmadalavalasaHibiscus2 Malvastrum leaf curl Mesta yellow vein mosaic 007 Guangdong virus virus DNA-A Ludwigia yellow vein virus- Malvastrum leaf curl virus- Methanobacterium phage associated DNA beta associated defective DNA psiM2 Ludwigia yellow vein virus beta Methanothermobacter DNA-A Malvastrum leaf curl virus-G87 prophage psiM100 Luffa begomovirus associated Malvastrum yellow mosaic Microbacterium phage Min1 DNA beta virus-associated DNA 1 Microcystis phage Ma-LMM01 Luffa puckering and leaf Malvastrum yellow mosaic Microplitis demolitor distortion-associated DNA virus DNA-A bracovirus segment A beta Malvastrum yellow mosaic Microplitis demolitor LuIII virus virus satellite DNA beta bracovirus segment B Lumpy skin disease virus NI- Malvastrum yellow vein Microplitis demolitor 2490 Baoshan virus DNA-A bracovirus segment C Lymantria dispar MNPV Malvastrum yellow vein-virus Microplitis demolitor Lymantria xylina MNPV Malvastrum yellow vein virus bracovirus segment D Lymphocystis disease virus 1 satellite DNA beta Microplitis demolitor Lymphocystis disease virus- Malvastrum yellow vein bracovirus segment E isolate China Yunnan-virus Microplitis demolitor Macacine herpesvirus 1 Malvastrum yellow vein bracovirus segment F Macacine herpesvirus 3 Yunnan virus satellite DNA Microplitis demolitor Macacine herpesvirus 4 beta bracovirus segment G Macacine herpesvirus 5 Mamestra configurata NPV-A Microplitis demolitor Macaque simian foamy virus Mamestra configurata NPV-B bracovirus segment H Macroptilium golden mosaic Mannheimia phage Microplitis demolitor virus- phiMHaA1 bracovirus segment I JamaicaWissadulaAugust Maruca vitrata MNPV Microplitis demolitor Town DNA A Mastomys coucha bracovirus segment J Macroptilium golden mosaic papillomavirus 2 Microplitis demolitor virus- bracovirus segment K

27 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Microplitis demolitor Mungbean yellow mosaic Mycobacterium phage bracovirus segment L India virus DNA A Che9c Microplitis demolitor Mungbean yellow mosaic Mycobacterium phage bracovirus segment M India virus DNA B Che9d Microplitis demolitor Mungbean yellow mosaic Mycobacterium phage Cjw1 bracovirus segment N virus DNA A Mycobacterium phage Microplitis demolitor Mungbean yellow mosaic Cooper bracovirus segment O virus DNA B Mycobacterium phage Milk vetch dwarf virus Murid herpesvirus 1 Corndog segment 10 Murid herpesvirus 2 Mycobacterium phage CrimD Milk vetch dwarf virus Murid herpesvirus 4 Mycobacterium phage D29 segment 11 Murine adenovirus 3 Mycobacterium phage DD5 Milk vetch dwarf virus Murine adenovirus A Mycobacterium phage ET08 segment-1 Murine pneumotropic virus Mycobacterium phage Milk vetch dwarf virus Murine polyomavirus Fruitloop segment 2 Murine type C retrovirus Mycobacterium phage Giles Milk vetch dwarf virus Musca domestica salivary Mycobacterium phage segment 3 gland hypertrophy virus Gumball Milk vetch dwarf virus Muscovy duck circovirus Mycobacterium phage Halo segment 4 Muscovy duck parvovirus Mycobacterium phage Milk vetch dwarf virus Mus musculus papillomavirus Jasper segment 5 type 1 Mycobacterium phage KBG Milk vetch dwarf virus Mycobacterium phage 244 Mycobacterium phage segment 6 Mycobacterium phage Konstantine Milk vetch dwarf virus Adjutor Mycobacterium phage segment 7 Mycobacterium phage Angel Kostya Milk vetch dwarf virus Mycobacterium phage Mycobacterium phage L5 segment 8 angelica Mycobacterium phage Milk vetch dwarf virus Mycobacterium phage LeBron segment 9 Ardmore Mycobacterium phage Llij Mimosa yellow leaf curl virus- Mycobacterium phage Mycobacterium phage associated DNA 1 Barnyard Lockley Mimosa yellow leaf curl virus Mycobacterium phage Mycobacterium phage DNA-A Bethlehem Myrna Mimosa yellow leaf curl virus Mycobacterium phage Mycobacterium phage Nigel satellite DNA beta Boomer Mycobacterium phage Minute virus of mice Mycobacterium phage BPs Omega Mirabilis mosaic virus Mycobacterium phage Brujita Mycobacterium phage Orion Miscanthus streak virus-91 Mycobacterium phage Mycobacterium phage Molluscum contagiosum virus Butterscotch Pacc40 subtype 1 Mycobacterium phage Bxb1 Mycobacterium phage PBI1 Monkeypox virus Zaire-96-I-16 Mycobacterium phage Bxz1 Mycobacterium phage Morganella phage MmP1 Mycobacterium phage Bxz2 Peaches Mouse mammary tumor virus Mycobacterium phage Cali Mycobacterium phage PG1 Mouse parvovirus 1 Mycobacterium phage Mycobacterium phage Mouse parvovirus 2 Catera Phaedrus Mouse parvovirus 3 Mycobacterium phage Chah Mycobacterium phage Phlyer Mouse parvovirus 4 Mycobacterium phage Mycobacterium phage Mouse parvovirus 5 Che12 Pipefish Mulard duck circovirus Mycobacterium phage Che8 Mycobacterium phage PLot Mycobacterium phage PMC

28 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Mycobacterium phage Porky Okra yellow mosaic Mexico Pelargonium vein banding Mycobacterium phage virus DNA B virus Predator Okra yellow vein disease Penaeus merguiensis Mycobacterium phage associated sequence virion densovirus Pukovnik Okra yellow vein mosaic virus Penaeus monodon Mycobacterium phage Old World harvest mouse hepatopancreatic parvovirus Qyrzula papillomavirus Pepper curly top virus Mycobacterium phage Orangutan polyomavirus Pepper golden mosaic virus Ramsey Orf virus DNA A Mycobacterium phage Rizal Orgyia leucostigma NPV Pepper golden mosaic virus Mycobacterium phage Orgyia pseudotsugata MNPV DNA B Rosebush Oryctes rhinoceros virus Pepper huasteco yellow vein Mycobacterium phage Ostreid herpesvirus 1 virus DNA A ScottMcG Ostreococcus tauri virus 1 Pepper huasteco yellow vein Mycobacterium phage Solon Ostreococcus virus OsV5 virus DNA B Mycobacterium phage Spud Ovine adenovirus A Pepper leaf curl Bangladesh Mycobacterium phage TM4 Ovine adenovirus D virus segment A component Mycobacterium phage Troll4 Ovine herpesvirus 2 Pepper leaf curl virus DNA-A Mycobacterium phage Ovine papillomavirus-1 Pepper leaf curl virus satellite Tweety Panicum streak virus-Karino DNA beta Mycobacterium phage U2 Panine herpesvirus 2 strain Pepper leaf curl Yunnan virus Mycobacterium phage Heberling satellite DNA beta Wildcat Papaya leaf curl China virus- Pepper leaf curl Yunnan virus- Mycoplasma phage MAV1 G8 YN323 Mycoplasma phage P1 Papaya leaf curl China virus Pepper yellow dwarf virus- Mycoplasma phage phiMFV1 satellite DNA beta New Mexico Myotis polyomavirus VM-2008 Papaya leaf curl Guandong Pepper yellow leaf curl Mythimna loreyi densovirus virus-GD2 DNA A Indonesia virus DNA-A Myxococcus phage Mx8 Papaya leaf curl virus- Pepper yellow leaf curl Myxoma virus associated DNA beta Indonesia virus DNA-B Myzus persicae densovirus Papaya leaf curl-virus Pepper yellow vein Mali virus Nanovirus-like particle Papiine herpesvirus 2 Periplaneta fuliginosa Natrialba phage PhiCh1 Paramecium bursaria densovirus Neodiprion abietis NPV Chlorella virus 1 Petunia vein clearing virus Neodiprion lecontei NPV Paramecium bursaria Phage cdtI Neodiprion sertifer NPV Chlorella virus AR158 Phage Gifsy-1 Oat dwarf virus Paramecium bursaria Phage Gifsy-2 OkLCV satDNA 10 Chlorella virus FR483 Phage phiJL001 Okra leaf curl disease Paramecium bursaria Phocoena spinipinnis associated DNA 1 Chlorella virus NY2A papillomavirus Okra leaf curl Mali virus Parvovirus H1 Phormidium phage Pf-WMP3 satellite DNA beta Passionfruit severe leaf Phormidium phage Pf-WMP4 Okra leaf curl virus-Cameroon distortion virus DNA-A Phthorimaea operculella Okra mottle virus-Brazilokra Passionfruit severe leaf granulovirus DNA A distortion virus DNA-B Pieris rapae granulovirus Okra mottle virus-Brazilokra Pasteurella phage F108 Planaria asexual strain- DNA B Peanut chlorotic streak virus specific virus-like element Okra yellow crinkle virus Pedilanthus leaf curl virus- type 1 large DNA segment segment A Pedilanthus Planaria asexual strain- Okra yellow mosaic Mexico PakistanMultan2004 specific virus-like element virus DNA A type 1 small DNA segment

29 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Planococcus citri densovirus Pseudomonas phage LBL3 Ranid herpesvirus 1 strain Plutella xylostella granulovirus Pseudomonas phage LIT1 McKinnell Plutella xylostella multiple Pseudomonas phage LKD16 Ranid herpesvirus 2 strain nucleopolyhedrovirus Pseudomonas phage LMA2 ATCC VR-568 Polyomavirus HPyV6 Pseudomonas phage LUZ19 Rauscher murine leukemia Polyomavirus HPyV7 Pseudomonas phage LUZ24 virus Porcine adenovirus C Pseudomonas phage LUZ7 Raven circovirus Porcine circovirus 1 Pseudomonas phage M6 RD114 retrovirus Porcine circovirus 2 Pseudomonas phage MP22 Reticuloendotheliosis virus Porcine endogenous Pseudomonas phage MP29 Rhesus monkey retrovirus E Pseudomonas phage MP38 papillomavirus Porcine parvovirus Pseudomonas phage PA11 Rhizobium phage 16-3 Potato apical leaf curl Pseudomonas phage PAJU2 Rhodothermus phage RM378 disease-associated satellite Pseudomonas phage Rhynchosia golden mosaic DNA beta PaP2Pseudomonas phage virus DNA A Potato yellow mosaic PaP3 Rhynchosia golden mosaic Panama virus DNA A Pseudomonas phage PB1 virus DNA B Potato yellow mosaic Pseudomonas phage Pf1 Rhynchosia golden mosaic Panama virus DNA B Pseudomonas phage Pf3 Yucatan virus DNA A Potato yellow mosaic Trinidad Pseudomonas phage phi-2 Rhynchosia golden mosaic virus DNA A Pseudomonas phage phiCTX Yucatan virus DNA B Potato yellow mosaic Trinidad Pseudomonas phage phikF77 Rice tungro bacilliform virus virus DNA B Pseudomonas phage phiKMV Roseobacter phage SIO1 Potato yellow mosaic virus Pseudomonas phage phiKZ Roseophage DSS3P2 DNA A Pseudomonas phage PT2 Roseophage EE36P1 Potato yellow mosaic virus Pseudomonas phage PT5 Rosss goose hepatitis B virus DNA B Pseudomonas phage SN Rousettus aegyptiacus Prochlorococcus phage P- Pseudomonas phage YuA papillomavirus type 1 SSM4 Psittacid herpesvirus 1 Rudbeckia flower distortion Propionibacterium phage B5 Psittacus erithacus timneh virus Propionibacterium phage papillomavirus Saccharum streak virus PA6 Pumpkin yellow mosaic Saimiriine herpesvirus 2 Pseudaletia unipuncta Malaysia virus DNA A Salmonella enterica granulovirus Pyrobaculum spherical virus bacteriophage SE1 Pseudoalteromonas phage Pyrococcus abyssi virus 1 Salmonella phage c341 PM2 Rabbit fibroma virus Salmonella phage E1 Pseudocowpox virus Rabbit oral papillomavirus Salmonella phage epsilon34 Pseudomonas phage 119X Rachiplusia ou MNPV Salmonella phage Fels-1 Pseudomonas phage 14-1 Radish leaf curl virus satellite Salmonella phage phiSG-JL2 Pseudomonas phage DNA beta Salmonella phage SETP3 201phi2-1 Radish leaf curl virus segment Salmonella phage ST64B Pseudomonas phage 73 A Sclerotinia sclerotiorum Pseudomonas phage B3 Ralstonia phage p12J hypovirulence associated Pseudomonas phage D3112 Ralstonia phage phiRSA1 DNA virus 1 Pseudomonas phage-D3 Ralstonia phage RSB1 Sea turtle tornovirus 1 Pseudomonas phage DMS3 Ralstonia phage RSL1 Senecio yellow mosaic virus Pseudomonas phage EL Ralstonia phage RSM1 Sheeppox virus 17077-99 Pseudomonas phage F10 Ralstonia phage RSM3 Sheldgoose hepatitis B virus Pseudomonas phage F116 Ralstonia phage RSS1 Shigella phage phiSboM-AG3 Pseudomonas phage F8 Ramie mosaic virus DNA-A Shrimp white spot syndrome Pseudomonas phage gh-1 Ramie mosaic virus DNA-B virus

30 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Sida golden mosaic Costa Sida yellow vein Vietnam virus Spiroplasma phage SVTS2 Rica virus DNA A satellite DNA beta Spodoptera exigua MNPV Sida golden mosaic Costa Sida yellow vein virus DNA A Spodoptera frugiperda Rica virus DNA B Sida yellow vein virus DNA B ascovirus 1a Sida golden mosaic Florida Sida yellow vein virus satellite Spodoptera frugiperda MNPV virus-Malvastrum DNA-A DNA beta virus Sida golden mosaic Florida Siegesbeckia yellow vein Spodoptera litura granulovirus virus-Malvastrum DNA-B Guangxi virus Spodoptera litura NPV Sida golden mosaic Honduras Siegesbeckia yellow vein Spodoptera litura virus DNA A virus-GD13-associated DNA nucleopolyhedrovirus II Sida golden mosaic Honduras beta Sputnik virophage virus DNA B Siegesbeckia yellow vein virus Squash leaf curl China virus-B Sida golden mosaic virus GD13 DNA-A DNA-A Simian adenovirus 1 Squash leaf curl China virus-B Sida golden mosaic virus Simian adenovirus 3 DNA B DNA-B Simian foamy virus 3 Squash leaf curl Philippines Sida golden mottle virus DNA- Simian immunodeficiency virus segment A A virus SIV-mnd 2 Squash leaf curl Philippines Sida golden mottle virus DNA- Simian retrovirus 4 virus segment B B Simian T-cell lymphotropic Squash leaf curl virus A Sida leaf curl virus-associated virus 6 component DNA DNA 1 Simian T-lymphotropic virus 1 Squash leaf curl virus B Sida leaf curl virus-associated Simian T-lymphotropic virus 3 component DNA DNA beta Simian virus 40 Squash leaf curl Yunnan virus Sida leaf curl-virus Singapore grouper iridovirus Squash mild leaf curl virus- Sida leaf curl virus satellite Sinorhizobium phage PBC5 Imperial Valley DNA A DNA beta Small anellovirus 1 Squash mild leaf curl virus- Sida micrantha mosaic virus Small anellovirus 2 Imperial Valley DNA B segment A Snake parvovirus 1 Squash yellow mild mottle Sida micrantha mosaic virus Snow goose hepatitis B virus virus DNA B segment B Sodalis phage phiSG1 Squirrel monkey polyomavirus Sida mosaic Sinaloa virus DNA Sodalis phage SO-1 Sri Lankan cassava mosaic A South African cassava mosaic virus DNA A Sida mosaic Sinaloa virus DNA virus DNA A Sri Lankan cassava mosaic B South African cassava mosaic virus DNA B Sida mottle virus virus DNA B Stachytarpheta leaf curl virus Sida yellow mosaic virus- Soybean chlorotic blotch virus Staphylococcus phage 11 China-associated DNA beta DNA A Staphylococcus phage 187 DNA beta Soybean chlorotic blotch virus Staphylococcus phage 2638A Sida yellow mosaic-virus DNA B Staphylococcus phage 29 Sida yellow mosaic Yucatan Soybean chlorotic mottle virus Staphylococcus phage 37 virus DNA A Soybean crinkle leaf virus Staphylococcus phage 3A Sida yellow mosaic Yucatan Soybean mild mottle virus Staphylococcus phage 42e virus DNA B Spilanthes yellow vein virus Staphylococcus phage Sida yellow vein disease DNA-A 44AHJD associated DNA 1 Spinach curly top virus Staphylococcus phage 47 Sida yellow vein Madurai virus Spiroplasma kunkelii virus SkV1 Staphylococcus phage 52A Sida yellow vein Vietnam CR2-3x Staphylococcus phage 53 virus-associated DNA 1 Spiroplasma phage 1-C74 Staphylococcus phage 55 Sida yellow vein Vietnam virus Spiroplasma phage 1-R8A2B Staphylococcus phage 66 DNA-A Spiroplasma phage 4 Staphylococcus phage 69

31 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Staphylococcus phage 71 Staphylococcus prophage Streptococcus prophage Staphylococcus phage 77 phi 12 MM1 Staphylococcus phage Staphylococcus prophage Streptococcus pyogenes 80alpha phi 13 phage 315.3 Staphylococcus phage 85 Staphylococcus prophage Streptomyces phage mu16 Staphylococcus phage 88 phiN315 Streptomyces phage phiBT1 Staphylococcus phage 92 Staphylococcus prophage Streptomyces phage phiC31 Staphylococcus phage 96 phiPV83 Streptomyces phage Staphylococcus phage Staphylococcus prophage phiSASD1 CNPH82 PVL Streptomyces phage VWB Staphylococcus phage EW Staphylococcus prophage Stx1 converting phage Staphylococcus phage G1 tp310-1 Stx2-converting phage 1717 Staphylococcus phage K Staphylococcus prophage Stx2-converting phage 86 Staphylococcus phage P954 tp310-2 Stx2 converting phage-I Staphylococcus phage PH15 Staphylococcus prophage Stx2 converting phage II Staphylococcus phage tp310-3 Subterranean clover stunt phi2958PVL Starling circovirus virus DNA 1 Staphylococcus phage Stenotrophomonas phage Subterranean clover stunt phiETA2 phiSMA9 virus DNA 2 Staphylococcus phage Stenotrophomonas phage S1 Subterranean clover stunt phiETA3 Strawberry vein banding virus virus DNA 3 Staphylococcus phage- Streptococcus phage 2972 Subterranean clover stunt phiETA Streptococcus phage 5093 virus DNA 4 Staphylococcus phage Streptococcus phage 7201 Subterranean clover stunt phiMR11 Streptococcus phage 858 virus DNA 5 Staphylococcus phage Streptococcus phage Abc2 Subterranean clover stunt phiMR25 Streptococcus phage virus DNA 6 Staphylococcus phage ALQ13.2 Subterranean clover stunt phiNM1 Streptococcus phage C1 virus DNA 7 Staphylococcus phage Streptococcus phage Cp-1 Subterranean clover stunt phiNM3 Streptococcus phage DT1 virus DNA 8 Staphylococcus phage Streptococcus phage M102 Sugarcane bacilliform IM virus phiP68 Streptococcus phage O1205 Sugarcane bacilliform Mor Staphylococcus phage Streptococcus phage P9 virus phiPVL108 Streptococcus phage PH10 Sugarcane bacilliform virus Staphylococcus phage Streptococcus phage PH15 Sugarcane streak Egypt virus- phiPVL-CN125 Streptococcus phage phi3396 Giza Staphylococcus phage Streptococcus phage Sfi11 Sugarcane streak Reunion phiSauS-IPLA35 Streptococcus phage Sfi19 virus Staphylococcus phage Streptococcus phage Sfi21 Sugarcane streak virus-Natal phiSauS-IPLA88 Streptococcus phage SM1 Suid herpesvirus 1 Staphylococcus phage phiSLT Streptococcus phage SMP Sulfolobus islandicus Staphylococcus phage Streptococcus prophage filamentous virus PT1028 315.1 Sulfolobus islandicus rod- Staphylococcus phage ROSA Streptococcus prophage shaped virus 1 Staphylococcus phage SAP- 315.2 Sulfolobus islandicus rod- 26 Streptococcus prophage shaped virus 2 Staphylococcus phage SAP2 315.5 Sulfolobus spindle-shaped Staphylococcus phage Twort Streptococcus prophage virus 4 Staphylococcus phage X2 315.6 Sulfolobus spindle-shaped Streptococcus prophage EJ-1 virus 5

32 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Sulfolobus spindle-shaped Tobacco curly shoot-virus Tomato leaf curl Cebu virus virus 6 Tobacco leaf curl disease DNA-A Sulfolobus spindle-shaped associated sequence virion Tomato leaf curl China virus- virus 7 Tobacco leaf curl Japan virus G32 Sulfolobus turreted Tobacco leaf curl Kochi virus Tomato leaf curl Cotabato icosahedral virus 2 Tobacco leaf curl Thailand virus DNA-A Sulfolobus turreted virus Tomato leaf curl Ghana virus icosahedral-virus Tobacco leaf curl virus- segment A Sulfolobus virus 1 associated DNA beta Tomato leaf curl Guangdong Sulfolobus virus 2 Tobacco leaf curl Yunnan virus DNA-A Sulfolobus virus Kamchatka 1 virus associated DNA 1 Tomato leaf curl Guangxi virus Sulfolobus virus Ragged Hills Tobacco leaf curl Yunnan Tomato leaf curl Gujarat virus- Sulfolobus virus STSV1 virus satellite DNA beta Varanasi segment A Sunn hemp leaf distortion virus Tobacco leaf curl Yunnan Tomato leaf curl Gujarat virus- DNA-A virus-Y136 Varanasi segment B Sus scrofa papillomavirus type Tobacco leaf curl Zimbabwe Tomato leaf curl Hainan virus 1 virus Tomato leaf curl Hsinchu virus- Sweetpotato badnavirus B Tobacco vein clearing virus TaiwanHsinchu2005 DNA A Sweet potato leaf curl Bengal Tobacco yellow dwarf virus Tomato leaf curl Iran virus virus-IndiaWest Bengal2008 Tomato begomovirus satellite Tomato leaf curl Java virus- segment A DNA beta Ageratum satellite DNA Sweet potato leaf curl Canary Tomato chino La Paz virus Tomato leaf curl Java-virus virus segment A Tomato leaf curl Joydebpur Sweet potato leaf curl Tomato chlorotic mottle virus beta virus Georgia virus DNA A Tomato leaf curl Joydebpur Sweet potato leaf curl Tomato chlorotic mottle virus virus DNA-A Lanzarote virus DNA B Tomato leaf curl Karnataka Sweet potato leaf curl Spain Tomato common mosaic virus virus-associated DNA beta virus DNA-A DNA-A Sweet potato leaf curl virus Tomato common mosaic virus Tomato leaf curl Karnataka- Swinepox virus DNA-B virus Synechococcus phage P60 Tomato curly stunt virus Tomato leaf curl Kerala virus Synechococcus phage S-PM2 Tomato golden mosaic virus Tomato leaf curl Kumasi virus Synechococcus phage S- DNA A segment A RSM4 Tomato golden mosaic virus Tomato leaf curl Laos virus Synechococcus phage syn9 DNA B Tomato leaf curl Malaysia Tanapox virus Tomato golden mottle virus virus Taro bacilliform virus DNA A Tomato leaf curl Mali virus Taterapox virus Tomato golden mottle virus Tomato leaf curl Mayotte virus Thalassomonas phage BA3 DNA B Tomato leaf curl Mindanao Thermoproteus tenax Tomato leaf curl Arusha virus virus DNA-A spherical virus 1 DNA-A Tomato leaf curl New Delhi Thermus phage IN93 Tomato leaf curl Bangalore virus-associated DNA beta Thermus phage P23-45 virus-Ban5 satellite DNA beta Tomato leaf curl New Delhi Thermus phage P23-77 Tomato leaf curl Bangalore- virus DNA A Thermus phage P74-26 virus Tomato leaf curl New Delhi Thermus phage phiYS40 Tomato leaf curl Bangladesh virus DNA B Tobacco curly shoot virus virus Tomato leaf curl Nigeria virus- associated DNA 1 Tomato leaf curl Cameroon Nigeria2006 Tobacco curly shoot virus- virus- Tomato leaf curl Pakistan virus associated DNA beta CameroonBueaOkra2008 associated DNA 1

33 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Tomato leaf curl Pakistan virus Tomato mottle Taino virus Tomato yellow spot virus DNA- segment A DNA B B Tomato leaf curl Palampur Tomato mottle virus DNA A Tomato yellow vein streak virus Tomato mottle virus DNA B virus DNA-A Tomato leaf curl Patna virus Tomato pseudo-curly top virus Tomato yellow vein streak DNA-A Tomato rugose mosaic virus virus DNA-B Tomato leaf curl Philippines DNA A Torque teno canis virus virus Tomato rugose mosaic virus Torque teno douroucouli virus Tomato leaf curl Philippine DNA B Torque teno felis virus virus satellite DNA beta Tomato severe leaf curl virus Torque teno midi virus 1 Tomato leaf curl Pune virus Tomato severe rugose virus Torque teno midi virus 2 Tomato leaf curl Seychelles DNA A Torque teno mini virus 1 virus Tomato severe rugose virus Torque teno mini virus 2 Tomato leaf curl Sinaloa virus DNA B Torque teno mini virus 3 DNA A Tomato yellow dwarf disease Torque teno mini virus 4 Tomato leaf curl Sinaloa virus associated satellite DNA Torque teno mini virus 5 DNA B beta-Kochi virus Torque teno mini virus 6 Tomato leaf curl Sri Lanka Tomato yellow leaf curl China Torque teno mini virus 7 virus virus associated DNA 1 Torque teno mini virus 8 Tomato leaf curl Sudan virus- Tomato yellow leaf curl Torque teno mini virus 9 Gezira China-virus Torque teno sus virus 1 Tomato leaf curl Sulawesi virus Tomato yellow leaf curl Torque teno tamarin virus DNA-A Guangdong virus DNA-A Torque teno virus 10 Tomato leaf curl Taiwan virus Tomato yellow leaf curl Torque teno virus 12 Tomato leaf curl Togo virus- Indonesia virus-Lembang Torque teno virus 14 Togo2006 Tomato yellow leaf curl Torque teno virus 15 Tomato leaf curl Vietnam virus Kanchanaburi virus DNA A Torque teno virus 16 DNA A Tomato yellow leaf curl Torque teno virus 19 Tomato leaf curl virus- Kanchanaburi virus DNA B Torque teno virus-1 associated DNA beta Tomato yellow leaf curl Mali Torque teno virus 25 Tomato leaf curl-virus virus-associated DNA beta Torque teno virus 26 Tomato leaf curl virus-Pune- Tomato yellow leaf curl Torque teno virus 27 associated DNA beta DNA-A Thailand virus associated DNA Torque teno virus 28 Tomato mild mosaic virus 1 Torque teno virus 3 DNA-A Tomato yellow leaf curl Torque teno virus 4 Tomato mild mosaic virus Thailand virus DNA A Torque teno virus 6 DNA-B Tomato yellow leaf curl Torque teno virus 7 Tomato mild yellow leaf curl Thailand virus DNA B Torque teno virus 8 Aragua virus DNA A Tomato yellow leaf curl Trichodysplasia spinulosa- Tomato mild yellow leaf curl Vietnam virus DNA-A associated polyomavirus Aragua virus DNA B Tomato yellow leaf curl Trichoplusia ni ascovirus 2c Tomato mosaic Havana virus Vietnam virus satellite DNA Trichoplusia ni SNPV DNA A beta Tupaiid herpesvirus 1 Tomato mosaic Havana virus Tomato yellow leaf curl virus- Turkey adenovirus A DNA B associated DNA beta Turnip curly top virus Tomato mosaic leaf curl virus Tomato yellow margin leaf TYLCCNV-Y322 satellite DNA DNA A curl virus DNA A beta Tomato mosaic leaf curl virus Tomato yellow margin leaf Urochloa streak virus DNA B curl virus DNA B Vaccinia virus Tomato mottle Taino virus Tomato yellow spot virus DNA- Variola virus DNA A A

34 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Velvet bean severe mosaic Vibrio phage VP2 Xanthomonas phage phiL7 virus DNA A Vibriophage VP4 Xanthomonas phage Xop411 Velvet bean severe mosaic Vibrio phage VP5 Xanthomonas phage Xp10 virus DNA B Vibrio phage VP882 Xanthomonas phage Xp15 Vernonia yellow vein Vibrio phage VP93 Xenopus laevis endogenous betasatellite Vibrio phage VpV262 retrovirus Xen1 Vernonia yellow vein virus Vibrio phage VSK Xestia c-nigrum granulovirus DNA-A Watermelon chlorotic stunt Xylella phage Xfas53 Vibrio phage fs1 virus DNA A Yaba-like disease virus Vibrio phage fs2 Watermelon chlorotic stunt Yaba monkey tumor virus Vibrio phage K139 virus DNA B Yersinia pestis phage Vibrio phage kappa Wheat dwarf virus phiA1122 Vibrio phage KSF-1phi Wissadula golden mosaic St Yersinia phage Berlin Vibrio phage KVP40 Thomas Virus DNA A Yersinia phage L-413C Vibrio phage N4 Wissadula golden mosaic St Yersinia phage phiYeO3-12 Vibrio phage VEJphi Thomas Virus DNA B Yersinia phage PY54 Vibrio phage Vf12 Woodchuck hepatitis virus Zinnia leaf curl disease Vibrio phage VfO3K6 WU Polyomavirus associated sequence virion Vibrio phage VfO4K68 Xanthomonas phage Cf1c Zinnia leaf curl virus- Vibrio phage VGJphi Xanthomonas phage OP1 associated DNA beta Vibrio phage VHML Xanthomonas phage OP2

35 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Appendix 3: Bacterial Database Acaryochloris marina Actinosynnema mirum DSM Anaerolinea thermophila UNI MBIC11017 43827 1 Acetobacter pasteurianus IFO Aerococcus urinae ACS 120 V Anaeromyxobacter 3283 01 Col10a dehalogenans 2CP 1 Acetohalobium arabaticum Aeromonas hydrophila subsp Anaeromyxobacter sp Fw109 DSM 5501 hydrophila ATCC 7966 5 Acholeplasma laidlawii PG 8A Aeromonas salmonicida Anaplasma centrale str Israel Achromobacter xylosoxidans subsp salmonicida A449 Anaplasma marginale str A8 Aeromonas veronii B565 Florida Acidaminococcus Aeropyrum pernix K1 Anaplasma phagocytophilum fermentans DSM 20731 Aggregatibacter HZ Acidaminococcus intestini actinomycetemcomitans Anoxybacillus flavithermus RyC MR95 D11S 1 WK1 Acidianus hospitalis W1 Aggregatibacter aphrophilus Aquifex aeolicus VF5 Acidilobus saccharovorans NJ8700 Arcanobacterium 345 15 Agrobacterium fabrum str haemolyticum DSM 20595 Acidimicrobium ferrooxidans C58 Archaeoglobus fulgidus DSM DSM 10331 Agrobacterium radiobacter 4304 Acidiphilium cryptum JF 5 K84 Archaeoglobus profundus Acidiphilium multivorum Agrobacterium sp H13 3 DSM 5631 AIU301 Agrobacterium vitis S4 Archaeoglobus veneficus Acidithiobacillus caldus SM 1 Akkermansia muciniphila SNP6 Acidithiobacillus ferrivorans ATCC BAA 835 Arcobacter butzleri RM4018 SS3 Alcanivorax borkumensis SK2 Arcobacter nitrofigilis DSM Acidithiobacillus ferrooxidans Alicycliphilus denitrificans BC 7299 ATCC 23270 Alicyclobacillus Arcobacter sp L Acidobacterium capsulatum acidocaldarius subsp Aromatoleum aromaticum ATCC 51196 acidocaldarius DSM 446 EbN1 Acidothermus cellulolyticus Aliivibrio salmonicida LFI1238 Arthrobacter arilaitensis Re117 11B Alkalilimnicola ehrlichii MLHE 1 Arthrobacter aurescens TC1 Acidovorax avenae subsp Alkaliphilus metalliredigens Arthrobacter avenae ATCC 19860 QYMF chlorophenolicus A6 Acidovorax citrulli AAC00 1 Alkaliphilus oremlandii OhILAs Arthrobacter Acidovorax ebreus TPSY Allochromatium vinosum DSM phenanthrenivorans Sphe3 Acidovorax sp JS42 180 Arthrobacter sp FB24 Aciduliprofundum boonei Alteromonas macleodii str Aster yellows witches broom T469 Deep ecotype phytoplasma AYWB Acinetobacter baumannii Alteromonas sp SN2 Asticcacaulis excentricus CB 1656 2 Aminobacterium 48 Acinetobacter calcoaceticus colombiense DSM 12261 Atopobium parvulum DSM PHEA 2 Ammonifex degensii KC4 20469 Acinetobacter oleivorans DR1 Amycolatopsis mediterranei Azoarcus sp BH72 Acinetobacter sp ADP1 U32 Azorhizobium caulinodans Actinobacillus Amycolicicoccus subflavus ORS 571 pleuropneumoniae serovar DQS3 9A1 Azospirillum sp B510 5b str L20 Anabaena variabilis ATCC Azotobacter vinelandii DJ Actinobacillus succinogenes 29413 Bacillus amyloliquefaciens 130Z Anaerococcus prevotii DSM DSM 7 Actinoplanes sp SE50 110 20548 Bacillus anthracis str Ames

36 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Bacillus atrophaeus 1942 Bifidobacterium animalis Burkholderia gladioli BSR3 Bacillus cellulosilyticus DSM subsp animalis ATCC 25527 Burkholderia glumae BGR1 2522 Bifidobacterium bifidum S17 Burkholderia mallei ATCC Bacillus cereus 03BB102 Bifidobacterium breve ACS 23344 Bacillus clausii KSM K16 071 V Sch8b Burkholderia multivorans Bacillus coagulans 2 6 Bifidobacterium dentium Bd1 ATCC 17616 Bacillus cytotoxicus NVH 391 Bifidobacterium longum Burkholderia phymatum 98 DJO10A STM815 Bacillus halodurans C 125 Blattabacterium sp Blattella Burkholderia phytofirmans Bacillus licheniformis DSM 13 germanica str Bge PsJN ATCC 14580 Bordetella avium 197N Burkholderia pseudomallei Bacillus megaterium DSM 319 Bordetella bronchiseptica 668 Bacillus mycoides DSM 2048 RB50 Burkholderia rhizoxinica HKI Bacillus pseudofirmus OF4 Bordetella parapertussis 12822 454 Bacillus pumilus SAFR 032 Bordetella pertussis CS Burkholderia sp 383 Bacillus selenitireducens Bordetella petrii DSM 12804 Burkholderia thailandensis MLS10 Borrelia afzelii PKo E264 Bacillus subtilis BSn5 Borrelia bissettii DN127 Burkholderia vietnamiensis G4 Bacillus thuringiensis serovar Borrelia burgdorferi B31 Burkholderia xenovorans berliner ATCC 10792 Borrelia duttonii Ly LB400 Bacillus weihenstephanensis Borrelia garinii PBi Butyrivibrio proteoclasticus KBAB4 Borrelia hermsii DAH B316 Bacteriovorax marinus SJ Borrelia recurrentis A1 Caldicellulosiruptor bescii Bacteroides fragilis YCH46 Borrelia turicatae 91E135 DSM 6725 Bacteroides helcogenes P 36 Brachybacterium faecium Caldicellulosiruptor 108 DSM 4810 hydrothermalis 108 Bacteroides salanitronis DSM Brachyspira hyodysenteriae Caldicellulosiruptor 18170 WA1 kristjanssonii 177R1B Bacteroides thetaiotaomicron Brachyspira intermedia PWS A Caldicellulosiruptor VPI 5482 Brachyspira murdochii DSM kronotskyensis 2002 Bacteroides vulgatus ATCC 12563 Caldicellulosiruptor 8482 Brachyspira pilosicoli 95 1000 lactoaceticus 6A Bartonella bacilliformis KC583 Bradyrhizobium japonicum Caldicellulosiruptor obsidiansis Bartonella clarridgeiae 73 USDA 110 OB47 Bartonella grahamii as4aup Bradyrhizobium sp BTAi1 Caldicellulosiruptor Bartonella henselae str Brevibacillus brevis NBRC owensensis OL Houston 1 100599 Caldicellulosiruptor Bartonella quintana str Brevundimonas subvibrioides saccharolyticus DSM 8903 Toulouse ATCC 15264 Calditerrivibrio nitroreducens Bartonella tribocorum CIP Brucella abortus A13334 DSM 19672 105476 Brucella canis ATCC 23365 Caldivirga maquilingensis IC Baumannia cicadellinicola str Brucella melitensis bv 1 str 16M 167 Hc Homalodisca coagulata Brucella microti CCM 4915 Campylobacter concisus Bdellovibrio bacteriovorus Brucella ovis ATCC 25840 13826 HD100 Brucella pinnipedialis B2 94 Campylobacter curvus 52592 Beijerinckia indica subsp Brucella suis 1330 Campylobacter fetus subsp indica ATCC 9039 Buchnera aphidicola str APS fetus 82 40 Beutenbergia cavernae DSM Acyrthosiphon pisum Campylobacter hominis 12333 Burkholderia ambifaria AMMD ATCC BAA 381 Bifidobacterium adolescentis Burkholderia cenocepacia Campylobacter jejuni subsp ATCC 15703 HI2424 jejuni 81116

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Campylobacter lari RM2100 Candidatus Solibacter usitatus Chlorobium Candidatus Accumulibacter Ellin6076 phaeobacteroides DSM 266 phosphatis clade IIA str UW 1 Candidatus Sulcia muelleri Chlorobium phaeovibrioides Candidatus Amoebophilus GWSS DSM 265 asiaticus 5a2 Candidatus Tremblaya Chlorobium tepidum TLS Candidatus Arthromitus sp SFB princeps PCIT Chloroflexus aggregans DSM mouse Japan Candidatus Vesicomyosocius 9485 Candidatus Azobacteroides okutanii HA Chloroflexus aurantiacus J 10 pseudotrichonymphae Candidatus Zinderia fl genomovar CFP2 insecticola CARI Chloroflexus sp Y 400 fl Candidatus Blochmannia Capnocytophaga canimorsus Chloroherpeton thalassium floridanus Cc5 ATCC 35110 Candidatus Carsonella ruddii Capnocytophaga ochracea Chromobacterium violaceum PV DSM 7271 ATCC 12472 Candidatus Carboxydothermus Chromohalobacter salexigens Chloracidobacterium hydrogenoformans Z 2901 DSM 3043 thermophilum B Carnobacterium sp 17 4 Citrobacter koseri ATCC BAA Candidatus Desulforudis Catenulispora acidiphila DSM 895 audaxviator MP104C 44928 Citrobacter rodentium ICC168 Candidatus Hamiltonella Caulobacter crescentus CB15 Clavibacter michiganensis defensa 5AT Acyrthosiphon Caulobacter segnis ATCC subsp michiganensis NCPPB pisum 21756 382 Candidatus Hodgkinia Caulobacter sp K31 Clostridium acetobutylicum cicadicola Dsem Cellulomonas fimi ATCC 484 ATCC 824 Candidatus Korarchaeum Cellulomonas flavigena DSM Clostridium beijerinckii NCIMB cryptofilum OPF8 20109 8052 Candidatus Koribacter Cellulophaga algicola DSM Clostridium botulinum A str versatilis Ellin345 14237 ATCC 3502 Candidatus Liberibacter Cellulophaga lytica DSM 7489 Clostridium cellulolyticum H10 asiaticus str psy62 Cellvibrio gilvus ATCC 13127 Clostridium cellulovorans 743B Candidatus Methylomirabilis Cellvibrio japonicus Ueda107 Clostridium difficile 630 oxyfera Cenarchaeum symbiosum A Clostridium kluyveri DSM 555 Candidatus Midichloria Chelativorans sp BNC1 Clostridium lentocellum DSM mitochondrii IricVA Chitinophaga pinensis DSM 5427 Candidatus Moranella 2588 Clostridium ljungdahlii DSM endobia PCIT Chlamydia muridarum Nigg 13528 Candidatus Nitrospira defluvii Chlamydia trachomatis 434 Clostridium novyi NT Candidatus Pelagibacter sp Bu Clostridium perfringens ATCC IMCC9063 Chlamydophila abortus S26 3 13124 Candidatus Phytoplasma Chlamydophila caviae GPIC Clostridium phytofermentans australiense Chlamydophila felis Fe C 56 ISDg Candidatus Protochlamydia Chlamydophila pecorum E58 Clostridium saccharolyticum amoebophila UWE25 Chlamydophila pneumoniae WM1 Candidatus Puniceispirillum CWL029 Clostridium sp SY8519 marinum IMCC1322 Chlamydophila psittaci 6BC Clostridium sticklandii DSM 519 Candidatus Riesia Chlorobaculum parvum NCIB Clostridium tetani E88 pediculicola USDA 8327 Clostridium thermocellum Candidatus Ruthia magnifica Chlorobium chlorochromatii ATCC 27405 str Cm Calyptogena CaD3 Collimonas fungivorans Ter331 magnifica Chlorobium limicola DSM 245 Colwellia psychrerythraea Chlorobium luteolum DSM 273 34H

38 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Comamonas testosteroni CNB Dechloromonas aromatica Desulfovibrio aespoeensis 2 RCB Aspo 2 Conexibacter woesei DSM Deferribacter desulfuricans Desulfovibrio africanus str 14684 SSM1 Walvis Bay Coprothermobacter Dehalococcoides Desulfovibrio alaskensis G20 proteolyticus DSM 5265 ethenogenes 195 Desulfovibrio desulfuricans Coraliomargarita akajimensis Dehalococcoides sp BAV1 ND132 DSM 45221 Dehalogenimonas Desulfovibrio magneticus RS 1 Coriobacterium glomerans lykanthroporepellens BL DC 9 Desulfovibrio salexigens DSM PW2 Deinococcus deserti VCD115 2638 Corynebacterium Deinococcus geothermalis Desulfovibrio vulgaris RCH1 aurimucosum ATCC 700975 DSM 11300 Desulfurispirillum indicum S5 Corynebacterium diphtheriae Deinococcus maricopensis Desulfurivibrio alkaliphilus NCTC 13129 DSM 21211 AHT2 Corynebacterium efficiens YS Deinococcus proteolyticus Desulfurobacterium 314 MRP thermolithotrophum DSM Corynebacterium Deinococcus radiodurans R1 11699 glutamicum ATCC 13032 Delftia acidovorans SPH 1 Desulfurococcus Corynebacterium jeikeium Delftia sp Cs1 4 kamchatkensis 1221n K411 Denitrovibrio acetiphilus DSM Desulfurococcus mucosus Corynebacterium 12809 DSM 2162 kroppenstedtii DSM 44385 Desulfarculus baarsii DSM Dichelobacter nodosus Corynebacterium 2075 VCS1703A pseudotuberculosis FRC41 Desulfatibacillum alkenivorans Dickeya dadantii 3937 Corynebacterium resistens AK 01 Dickeya zeae Ech1591 DSM 45100 Desulfitobacterium hafniense Dictyoglomus thermophilum H Corynebacterium ulcerans Y51 6 12 809 Desulfobacca acetoxidans Dictyoglomus turgidum DSM Corynebacterium urealyticum DSM 11109 6724 DSM 7109 Desulfobacterium Dinoroseobacter shibae DFL Corynebacterium variabile autotrophicum HRM2 12 DSM 44702 Desulfobulbus propionicus Dyadobacter fermentans Coxiella burnetii RSA 493 DSM 2032 DSM 18053 Croceibacter atlanticus Desulfococcus oleovorans Edwardsiella ictaluri 93 146 HTCC2559 Hxd3 Edwardsiella tarda EIB202 Cronobacter sakazakii ATCC Desulfohalobium retbaense Eggerthella lenta DSM 2243 BAA 894 DSM 5692 Eggerthella sp YY7918 Cronobacter turicensis z3032 Desulfomicrobium baculatum Ehrlichia canis str Jake Cryptobacterium curtum DSM DSM 4028 Ehrlichia chaffeensis str 15641 Desulfotalea psychrophila Arkansas Cupriavidus metallidurans LSv54 Ehrlichia ruminantium str CH34 Desulfotomaculum Welgevonden Cupriavidus necator N 1 acetoxidans DSM 771 Elusimicrobium minutum Cupriavidus taiwanensis LMG Desulfotomaculum Pei191 19424 carboxydivorans CO 1 SRB Enterobacter aerogenes cyanobacterium UCYN A Desulfotomaculum kuznetsovii KCTC 2190 Cyanothece sp ATCC 51142 DSM 6115 Enterobacter asburiae LF7a Cyclobacterium marinum Desulfotomaculum reducens Enterobacter cloacae subsp DSM 745 MI 1 cloacae ATCC 13047 Cytophaga hutchinsonii Desulfotomaculum ruminis Enterobacter sp 638 ATCC 33406 DSM 2154 Enterococcus faecalis V583

39 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Erwinia amylovora ATCC Francisella tularensis subsp Granulicella mallensis 49946 holarctica LVS MP5ACTX8 Erwinia billingiae Eb661 Frankia alni ACN14a Granulicella tundricola Erwinia pyrifoliae DSM 12163 Frankia sp CcI3 Haemophilus ducreyi 35000HP Erwinia sp Ejp617 Frankia symbiont of Datisca Haemophilus influenzae 10810 Erwinia tasmaniensis Et1 99 glomerata Haemophilus parainfluenzae Erysipelothrix rhusiopathiae Fusobacterium nucleatum T3T1 Erythrobacter litoralis subsp nucleatum ATCC 25586 Haemophilus parasuis SH0165 HTCC2594 Gallibacterium anatis UMN179 Haemophilus somnus 129PT Escherichia coli O157:H7 str Gallionella capsiferriformans Hahella chejuensis KCTC 2396 Sakai ES 2 Halalkalicoccus jeotgali B3 Escherichia fergusonii ATCC gamma proteobacterium Halanaerobium 35469 HdN1 hydrogeniformans Ethanoligenens harbinense Gardnerella vaginalis 409 05 Haliangium ochraceum DSM YUAN 3 Gemmatimonas aurantiaca T 14365 Eubacterium eligens ATCC 27 Haliscomenobacter hydrossis 27750 Geobacillus kaustophilus DSM 1100 Eubacterium limosum KIST612 HTA426 Haloarcula hispanica ATCC Eubacterium rectale ATCC Geobacillus sp C56 T3 33960 33656 Geobacillus Haloarcula marismortui ATCC Exiguobacterium sibiricum 255 thermodenitrificans NG80 2 43049 15 Geobacillus Halobacterium sp NRC 1 Exiguobacterium sp AT1b thermoglucosidasius C56 YS93 Haloferax volcanii DS2 Ferrimonas balearica DSM Geobacillus thermoleovorans Halogeometricum 9799 CCB US3 UF5 borinquense DSM 11551 Ferroglobus placidus DSM Geobacter bemidjiensis Bem Halomicrobium mukohataei 10642 Geobacter daltonii FRC 32 DSM 12286 Fervidobacterium nodosum Geobacter lovleyi SZ Halomonas elongata DSM Rt17 B1 Geobacter metallireducens 2581 Fibrobacter succinogenes GS 15 halophilic archaeon DL31 subsp succinogenes S85 Geobacter sp M18 Halopiger xanaduensis SH 6 Filifactor alocis ATCC 35896 Geobacter sulfurreducens Haloquadratum walsbyi C23 Finegoldia magna ATCC PCA Halorhabdus utahensis DSM 29328 Geobacter uraniireducens Rf4 12940 Flavobacteriaceae Geodermatophilus obscurus Halorhodospira halophila SL1 bacterium 3519 10 DSM 43160 Halorubrum lacusprofundi Flavobacterium Glaciecola nitratireducens ATCC 49239 branchiophilum FL 15 FR1064 Haloterrigena turkmenica Flavobacterium columnare Glaciecola sp 4H 3 7YE 5 DSM 5511 ATCC 49512 Gloeobacter violaceus PCC Halothermothrix orenii H 168 Flavobacterium johnsoniae 7421 Halothiobacillus neapolitanus UW101 Gluconacetobacter c2 Flavobacterium diazotrophicus PAl 5 Helicobacter acinonychis str psychrophilum JIP02 86 Gluconacetobacter xylinus Sheeba Flexistipes sinusarabici DSM NBRC 3288 Helicobacter bizzozeronii CIII 1 4947 Gluconobacter oxydans 621H Helicobacter felis ATCC 49179 Fluviicola taffensis DSM 16823 Gordonia bronchialis DSM Helicobacter hepaticus ATCC Francisella novicida U112 43247 51449 Francisella philomiragia subsp Gramella forsetii KT0803 Helicobacter mustelae 12198 philomiragia ATCC 25017 Granulibacter bethesdensis Helicobacter pylori 26695 Francisella sp TX077308 CGDNIH1

40 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Heliobacterium Kytococcus sedentarius DSM Legionella pneumophila modesticaldum Ice1 20547 subsp pneumophila ATCC Herbaspirillum seropedicae Lacinutrix sp 5H 3 7 4 43290 SmR1 Lactobacillus acidophilus Leifsonia xyli subsp xyli str Herminiimonas NCFM CTCB07 arsenicoxydans Lactobacillus amylovorus GRL Leptospira biflexa serovar Herpetosiphon aurantiacus 1112 Patoc strain Patoc 1 Ames DSM 785 Lactobacillus brevis ATCC 367 Leptospira borgpetersenii Hippea maritima DSM 10411 Lactobacillus buchneri NRRL B serovar Hardjo bovis str L550 Hirschia baltica ATCC 49814 30929 Leptospira interrogans serovar Hydrogenobacter Lactobacillus casei ATCC 334 Copenhageni str Fiocruz L1 thermophilus TK 6 Lactobacillus crispatus ST1 130 Hydrogenobaculum sp Lactobacillus delbrueckii Leptothrix cholodnii SP 6 Y04AAS1 subsp bulgaricus ATCC 11842 Leptotrichia buccalis C 1013 b Hyperthermus butylicus DSM Lactobacillus fermentum IFO Leuconostoc citreum KM20 5456 3956 Leuconostoc gasicomitatum Hyphomicrobium denitrificans Lactobacillus gasseri ATCC LMG 18811 ATCC 51888 33323 Leuconostoc kimchii IMSNU Hyphomicrobium sp Lactobacillus helveticus DPC 11154 Hyphomonas neptunium 4571 Leuconostoc mesenteroides ATCC 15444 Lactobacillus johnsonii NCC subsp mesenteroides ATCC Idiomarina loihiensis L2TR 533 8293 Ignicoccus hospitalis KIN4 I Lactobacillus kefiranofaciens Leuconostoc sp C2 Ignisphaera aggregans DSM ZW3 Listeria innocua Clip11262 17230 Lactobacillus plantarum Listeria ivanovii Ilyobacter polytropus DSM subsp plantarum ST III Listeria monocytogenes EGD 2926 Lactobacillus reuteri DSM e Intrasporangium calvum DSM 20016 Listeria seeligeri serovar 1 2b 43043 Lactobacillus rhamnosus str SLCC3954 Isoptericola variabilis 225 ATCC 8530 Listeria welshimeri serovar 6b Isosphaera pallida ATCC Lactobacillus ruminis ATCC str SLCC5334 43644 27782 Lysinibacillus sphaericus C3 41 Jannaschia sp CCS1 Lactobacillus sakei subsp Macrococcus caseolyticus Janthinobacterium sp sakei 23K JCSC5402 Marseille Lactobacillus salivarius Magnetococcus marinus MC Jonesia denitrificans DSM UCC118 1 20603 Lactobacillus sanfranciscensis Magnetospirillum Kangiella koreensis DSM 16069 TMW 11304 magneticum AMB 1 Ketogulonicigenium vulgare Lactococcus garvieae ATCC Mahella australiensis 50 1 BON WSH 001 49156 Mannheimia Kineococcus radiotolerans Lactococcus lactis subsp succiniciproducens MBEL55E SRS30216 cremoris NZ9000 Maribacter sp HTCC2170 Kitasatospora setae KM 6054 Laribacter hongkongensis Maricaulis maris MCS10 Klebsiella oxytoca KCTC 1686 HLHK9 Marinithermus hydrothermalis Klebsiella pneumoniae 342 Lawsonia intracellularis PHE DSM 14884 Klebsiella variicola At 22 MN1 00 Marinobacter adhaerens Kocuria rhizophila DC2201 Leadbetterella byssophila HP15 Kosmotoga olearia TBF 1951 DSM 17132 Marinobacter aquaeolei VT8 Kribbella flavida DSM 17836 Legionella longbeachae Marinomonas mediterranea Krokinobacter sp 4H 3 7 5 NSW150 MMB 1 Kyrpidia tusciae DSM 2912

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Marinomonas posidonica IVIA Methanohalobium Methylococcus capsulatus str Po 181 evestigatum Z 7303 Bath Marinomonas sp MWYL1 Methanohalophilus mahii DSM Methylomicrobium Marivirga tractuosa DSM 4126 5219 alcaliphilum Megasphaera elsdenii Methanoplanus petrolearius Methylomonas methanica Meiothermus ruber DSM 1279 DSM 11571 MC09 Meiothermus silvanus DSM Methanopyrus kandleri AV19 Methylotenera mobilis JLW8 9946 Methanoregula boonei 6A8 Methylotenera versatilis 301 Melissococcus plutonius ATCC Methanosaeta concilii GP6 Methylovorus glucosetrophus 35311 Methanosaeta thermophila PT SIP3 4 Mesoplasma florum L1 Methanosalsum zhilinae DSM Methylovorus sp MP688 Mesorhizobium ciceri biovar 4017 Micavibrio aeruginosavorus biserrulae WSM1271 Methanosarcina acetivorans ARL 13 Mesorhizobium loti C2A Microbacterium testaceum MAFF303099 Methanosarcina barkeri str StLB037 Mesorhizobium opportunistum Fusaro Micrococcus luteus NCTC WSM2075 Methanosarcina mazei Go1 2665 Metallosphaera cuprina Ar 4 Methanosphaera Microcystis aeruginosa NIES Metallosphaera sedula DSM stadtmanae DSM 3091 843 5348 Methanosphaerula palustris Microlunatus phosphovorus Methanobacterium sp AL 21 E1 9c NM 1 Methanobrevibacter Methanospirillum hungatei JF Micromonospora aurantiaca ruminantium 1 ATCC 27029 M1Methanobrevibacter Methanothermobacter Micromonospora sp L5 smithii ATCC 35061 marburgensis str Marburg Mobiluncus curtisii ATCC Methanocaldococcus Methanothermobacter 43063 fervens AG86 thermautotrophicus str Delta Moorella thermoacetica Methanocaldococcus H ATCC 39073 infernus ME Methanothermococcus Moraxella catarrhalis RH4 Methanocaldococcus okinawensis IH1 Muricauda ruestringensis DSM jannaschii DSM 2661 Methanothermus fervidus 13258 Methanocaldococcus sp DSM 2088 Mycobacterium abscessus FS406 22 Methanotorris igneus Kol 5 ATCC 19977 Methanocaldococcus Methylacidiphilum infernorum Mycobacterium africanum vulcanius M7 V4 GM041182 Methanocella arvoryzae Methylibium petroleiphilum Mycobacterium avium 104 MRE50 PM1 Mycobacterium bovis AF2122 Methanocella paludicola Methylobacillus flagellatus KT 97 SANAE Methylobacterium Mycobacterium canettii CIPT Methanococcoides burtonii chloromethanicum CM4 140010059 DSM 6242 Methylobacterium extorquens Mycobacterium gilvum PYR Methanococcus aeolicus AM1 GCK Nankai 3 Methylobacterium nodulans Mycobacterium leprae TN Methanococcus maripaludis ORS 2060 Mycobacterium marinum M S2 Methylobacterium populi Mycobacterium rhodesiae Methanococcus vannielii SB BJ001 NBB3 Methanococcus voltae A3 Methylobacterium Mycobacterium smegmatis str Methanocorpusculum radiotolerans JCM 2831 MC2 155 labreanum Z Methylobacterium sp 4 46 Mycobacterium sp JDM601 Methanoculleus marisnigri JR1 Methylocella silvestris BL2 Mycobacterium tuberculosis H37Rv

42 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Mycobacterium ulcerans Neisseria lactamica 020 06 Orientia tsutsugamushi str Agy99 Neisseria meningitidis M01 Boryong Mycobacterium vanbaalenii 240149 Oscillibacter valericigenes PYR 1 Neorickettsia risticii str Illinois Owenweeksia hongkongensis Mycoplasma agalactiae PG2 Neorickettsia sennetsu str DSM 17368 Mycoplasma arthritidis 158L3 1 Miyayama Paenibacillus mucilaginosus Mycoplasma bovis PG45 Niastella koreensis GR20 10 KNP414 Mycoplasma capricolum Nitratifractor salsuginis DSM Paenibacillus polymyxa E681 subsp capricolum ATCC 16511 Paenibacillus sp JDR 2 27343 Nitratiruptor sp SB155 2 Paenibacillus terrae HPL 003 Mycoplasma conjunctivae Nitrobacter hamburgensis X14 Paludibacter propionicigenes HRC 581 Nitrobacter winogradskyi Nb WB4 Mycoplasma crocodyli MP145 255 Pantoea ananatis LMG 20103 Mycoplasma gallisepticum str Nitrosococcus halophilus Nc4 Pantoea sp At 9b Rlow Nitrosococcus oceani ATCC Pantoea vagans C9 1 Mycoplasma genitalium G37 19707 Parabacteroides distasonis Mycoplasma haemocanis str Nitrosococcus watsonii C 113 ATCC 8503 Illinois Nitrosomonas europaea Parachlamydia Mycoplasma haemofelis str ATCC 19718 acanthamoebae UV 7 Langford 1 Nitrosomonas eutropha C91 Paracoccus denitrificans Mycoplasma hominis Nitrosomonas sp AL212 PD1222 Mycoplasma Nitrosopumilus maritimus Parvibaculum hyopneumoniae 232 SCM1 lavamentivorans DS 1 Mycoplasma hyorhinis HUB 1 Nitrosospira multiformis ATCC Parvularcula bermudensis Mycoplasma leachii 99 014 6 25196 HTCC2503 Mycoplasma mobile 163K Nocardia farcinica IFM 10152 Pasteurella multocida subsp Mycoplasma mycoides subsp Nocardioides sp JS614 multocida str Pm70 mycoides SC str PG1 Nocardiopsis dassonvillei Pectobacterium atrosepticum Mycoplasma penetrans HF 2 subsp dassonvillei DSM 43111 SCRI1043 Mycoplasma pneumoniae Nostoc azollae 0708 Pectobacterium carotovorum M129 Nostoc punctiforme PCC subsp carotovorum PC1 Mycoplasma pulmonis UAB 73102 Pectobacterium wasabiae CTIP Nostoc sp PCC 7120 WPP163 Mycoplasma putrefaciens KS1 Novosphingobium Pediococcus pentosaceus Mycoplasma suis str Illinois aromaticivorans DSM 12444 ATCC 25745 Mycoplasma synoviae 53 Novosphingobium sp PP1Y Pedobacter heparinus DSM Myxococcus fulvus HW 1 Oceanithermus profundus 2366 Myxococcus xanthus DK 1622 DSM 14977 Pedobacter saltans DSM Nakamurella multipartita DSM Oceanobacillus iheyensis 12145 44233 HTE831 Pelagibacterium halotolerans Nanoarchaeum equitans Kin4 Ochrobactrum anthropi B2 M ATCC 49188 Pelobacter carbinolicus DSM Natranaerobius thermophilus Odoribacter splanchnicus 2380 JW NM WN LF DSM 20712 Pelobacter propionicus DSM Natrialba magadii ATCC Oenococcus oeni PSU 1 2379 43099 Oligotropha carboxidovorans Pelodictyon Natronomonas pharaonis OM5 phaeoclathratiforme BU 1 DSM 2160 Olsenella uli DSM 7084 Pelotomaculum Nautilia profundicola AmH Onion yellows phytoplasma thermopropionicum SI Neisseria gonorrhoeae FA OY M Persephonella marina EX H1 1090 Opitutus terrae PB90 1 Petrotoga mobilis SJ95

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Phenylobacterium zucineum Pseudomonas Ramlibacter tataouinensis HLK1 brassicacearum subsp TTB310 Photobacterium profundum brassicacearum NFM421 Renibacterium salmoninarum SS9 Pseudomonas entomophila ATCC 33209 Photorhabdus asymbiotica L48 Rhizobium etli CFN 42 subsp asymbiotica ATCC Pseudomonas fluorescens Rhizobium leguminosarum bv 43949 F113 viciae 3841 Photorhabdus luminescens Pseudomonas fulva 12 X Rhodobacter capsulatus SB subsp laumondii TTO1 Pseudomonas mendocina 1003 Picrophilus torridus DSM 9790 ymp Rhodobacter sphaeroides 241 Pirellula staleyi DSM 6068 Pseudomonas protegens Pf 5 Rhodococcus equi 103S Planctomyces brasiliensis DSM Pseudomonas putida F1 Rhodococcus erythropolis PR4 5305 Pseudomonas stutzeri A1501 Rhodococcus jostii RHA1 Planctomyces limnophilus Pseudomonas syringae pv Rhodococcus opacus B4 DSM 3776 phaseolicola 1448A Rhodoferax ferrireducens T118 Polaromonas Pseudonocardia Rhodomicrobium vannielii naphthalenivorans CJ2 dioxanivorans CB1190 ATCC 17100 Polaromonas sp JS666 Pseudovibrio sp FO BEG1 Rhodopirellula baltica SH 1 Polymorphum gilvum SL003B Pseudoxanthomonas spadix Rhodopseudomonas palustris 26A1 BD a59 CGA009 Polynucleobacter necessarius Pseudoxanthomonas Rhodospirillum centenum SW subsp asymbioticus QLW suwonensis 11 1 Rhodospirillum rubrum ATCC P1DMWA 1 Psychrobacter arcticus 273 4 11170 Porphyromonas Psychrobacter cryohalolentis Rhodothermus marinus DSM asaccharolytica DSM 20707 K5 4252 Porphyromonas gingivalis W83 Psychrobacter sp PRwf 1 Rickettsia africae ESF 5 Prevotella denticola F0289 Psychromonas ingrahamii 37 Rickettsia akari str Hartford Prevotella melaninogenica Pusillimonas sp T7 7 Rickettsia bellii RML369 C ATCC 25845 Pyrobaculum aerophilum str Rickettsia canadensis str Prevotella ruminicola 23 IM2 McKiel Prochlorococcus marinus str Pyrobaculum arsenaticum Rickettsia conorii str Malish 7 MIT 9215 DSM 13514 Rickettsia felis URRWXCal2 Propionibacterium acnes Pyrobaculum calidifontis JCM Rickettsia heilongjiangensis 6609 11548 054 Propionibacterium Pyrobaculum islandicum DSM Rickettsia japonica YH freudenreichii subsp shermanii 4184 Rickettsia massiliae MTU5 CIRM BIA1 Pyrobaculum neutrophilum Rickettsia peacockii str Rustic Prosthecochloris aestuarii DSM V24Sta Rickettsia prowazekii str 271 Pyrobaculum sp 1860 Madrid E Proteus mirabilis HI4320 Pyrococcus abyssi GE5 Rickettsia rickettsii str Iowa Pseudoalteromonas atlantica Pyrococcus furiosus DSM 3638 Rickettsia sibirica 246 T6c Pyrococcus horikoshii OT3 Rickettsia slovaca 13 B Pseudoalteromonas Pyrococcus sp NA2 Rickettsia typhi str Wilmington haloplanktis TAC125 Pyrococcus yayanosii CH1 Riemerella anatipestifer ATCC Pseudoalteromonas sp Pyrolobus fumarii 1A 11845 DSM 15868 SM9913 Rahnella sp Y9602 Robiginitalea biformata Pseudogulbenkiania sp NH8B Ralstonia eutropha JMP134 HTCC2501 Pseudomonas aeruginosa Ralstonia pickettii 12D Roseburia hominis A2 183 PAO1 Ralstonia solanacearum Roseiflexus castenholzii DSM GMI1000 13941 Roseiflexus sp RS 1

44 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Roseobacter denitrificans Shewanella piezotolerans Stackebrandtia nassauensis OCh 114 WP3 DSM 44728 Roseobacter litoralis Och 149 Shewanella putrefaciens CN Staphylococcus aureus subsp Rothia dentocariosa ATCC 32 aureus JH1 17931 Shewanella sediminis HAW Staphylococcus carnosus Rothia mucilaginosa DY 18 EB3 subsp carnosus TM300 Rubrobacter xylanophilus Shewanella sp ANA 3 Staphylococcus epidermidis DSM 9941 Shewanella violacea DSS12 ATCC 12228 Ruegeria pomeroyi DSS 3 Shewanella woodyi ATCC Staphylococcus haemolyticus Ruegeria sp TM1040 51908 JCSC1435 Ruminococcus albus 7 Shigella boydii Sb227 Staphylococcus lugdunensis Runella slithyformis DSM 19594 Shigella dysenteriae Sd197 HKU09 01 Saccharomonospora viridis Shigella flexneri 2a str 301 Staphylococcus DSM 43017 Shigella sonnei Ss046 pseudintermedius HKU10 03 Saccharophagus degradans Sideroxydans lithotrophicus ES Staphylothermus hellenicus 2 40 1 DSM 12710 Saccharopolyspora erythraea Simkania negevensis Z Staphylothermus marinus F1 NRRL 2338 Sinorhizobium fredii NGR234 Starkeya novella DSM 506 Salinibacter ruber DSM 13855 Sinorhizobium medicae Stenotrophomonas Salinispora arenicola CNS 205 WSM419 maltophilia K279a Salinispora tropica CNB 440 Sinorhizobium meliloti 1021 Stigmatella aurantiaca DW4 3 Salmonella bongori NCTC Slackia heliotrinireducens DSM 1 12419 20476 Streptobacillus moniliformis Salmonella enterica subsp Sodalis glossinidius str DSM 12112 enterica serovar Enteritidis str morsitans Streptococcus agalactiae P125109 Sorangium cellulosum So ce56 2603V R Sanguibacter keddieii DSM Sphaerobacter thermophilus Streptococcus dysgalactiae 10542 DSM 20745 subsp equisimilis ATCC 12394 Sebaldella termitidis ATCC Sphaerochaeta coccoides Streptococcus equi 33386 DSM 17374 subspecies zooepidemicus Segniliparus rotundus DSM Sphaerochaeta globus str Streptococcus gallolyticus 44985 Buddy subsp gallolyticus ATCC BAA Selenomonas sputigena Sphaerochaeta pleomorpha 2069 ATCC 35185 str Grapes Streptococcus gordonii str Serratia plymuthica AS9 Sphingobacterium sp 21 Challis substr CH1 Serratia proteamaculans 568 Sphingobium Streptococcus macedonicus Serratia sp AS12 chlorophenolicum L 1 ACA DC 198 Serratia symbiotica str Cinara Sphingobium japonicum Streptococcus mitis B6 cedri UT26S Streptococcus mutans Shewanella amazonensis SB2B Sphingobium sp SYK 6 NN2025 Shewanella baltica OS155 Sphingomonas wittichii RW1 Streptococcus oralis Uo5 Shewanella denitrificans Sphingopyxis alaskensis Streptococcus parasanguinis OS217 RB2256 ATCC 15912 Shewanella frigidimarina Spirochaeta caldaria DSM Streptococcus parauberis NCIMB 400 7334 KCTC 11537 Shewanella halifaxensis HAW Spirochaeta smaragdinae Streptococcus pasteurianus EB4 DSM 11293 ATCC 43144 Shewanella loihica PV 4 Spirochaeta thermophila DSM Streptococcus pneumoniae Shewanella oneidensis MR 1 6192 ST556 Shewanella pealeana ATCC Spirosoma linguale DSM 74 Streptococcus 700345 pseudopneumoniae IS7493

45 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Streptococcus pyogenes M1 Synechocystis sp PCC 6803 Thermococcus GAS Syntrophobacter gammatolerans EJ3 Streptococcus salivarius fumaroxidans MPOB Thermococcus kodakarensis JIM8780 Syntrophobotulus glycolicus KOD1 Streptococcus sanguinis SK36 DSM 8271 Thermococcus onnurineus Streptococcus suis 05ZYH33 Syntrophomonas wolfei subsp NA1 Streptococcus thermophilus wolfei str Goettingen Thermococcus sibiricus MM CNRZ1066 Syntrophothermus lipocalidus 739 Streptococcus uberis 0140J DSM 12680 Thermococcus sp 4557 Streptomyces avermitilis MA Syntrophus aciditrophicus SB Thermocrinis albus DSM 14484 4680 Tannerella forsythia ATCC Thermodesulfatator indicus Streptomyces 43037 DSM 15286 bingchenggensis BCW 1 Taylorella equigenitalis MCE9 Thermodesulfobacterium sp Streptomyces cattleya NRRL Tepidanaerobacter OPB45 8057 DSM 46488 acetatoxydans Re1 Thermodesulfobium Streptomyces coelicolor A32 Teredinibacter turnerae T7901 narugense DSM 14796 Streptomyces flavogriseus Terriglobus saanensis SP1PR4 Thermodesulfovibrio ATCC 33331 Tetragenococcus halophilus yellowstonii DSM 11347 Streptomyces griseus subsp Thauera sp MZ1T Thermofilum pendens Hrk 5 griseus NBRC 13350 Thermaerobacter marianensis Thermomicrobium roseum Streptomyces scabiei 8722 DSM 12885 DSM 5159 Streptomyces sp SirexAA E Thermanaerovibrio Thermomonospora curvata Streptomyces violaceusniger acidaminovorans DSM 6589 DSM 43183 Tu 4113 Thermincola potens JR Thermoplasma acidophilum Streptosporangium roseum Thermoanaerobacter brockii DSM 1728 DSM 43021 subsp finnii Ako 1 Thermoplasma volcanium Sulfobacillus acidophilus DSM Thermoanaerobacter italicus GSS1 10332 Ab9 Thermoproteus uzoniensis 768 Sulfolobus acidocaldarius Thermoanaerobacterium 20 DSM 639 thermosaccharolyticum DSM Thermosediminibacter oceani Sulfolobus islandicus M1425 571 DSM 16646 Sulfolobus solfataricus P2 Thermoanaerobacterium Thermosipho africanus TCF52B Sulfolobus tokodaii str 7 xylanolyticum LX 11 Thermosipho melanesiensis Sulfuricurvum kujiense DSM Thermoanaerobacter BI429 16994 mathranii subsp mathranii str Thermosphaera aggregans Sulfurihydrogenibium A3 DSM 11486 azorense Az Fu1 Thermoanaerobacter Thermosynechococcus Sulfurihydrogenibium sp pseudethanolicus ATCC elongatus BP 1 YO3AOP1 33223 Thermotoga lettingae TMO Sulfurimonas autotrophica Thermoanaerobacter sp X513 Thermotoga maritima MSB8 DSM 16294 Thermoanaerobacter Thermotoga naphthophila Sulfurimonas denitrificans DSM tengcongensis MB4 RKU 10 1251 Thermoanaerobacter wiegelii Thermotoga neapolitana DSM Sulfurospirillum deleyianum Rt8B1 4359 DSM 6946 Thermobaculum terrenum Thermotoga petrophila RKU 1 Sulfurovum sp NBC37 1 ATCC BAA 798 Thermotoga sp RQ2 Symbiobacterium Thermobifida fusca YX Thermotoga thermarum DSM thermophilum IAM 14863 Thermobispora bispora DSM 5069 Synechococcus elongatus 43833 Thermovibrio ammonificans PCC 6301 Thermococcus barophilus MP HB 1 Synechococcus sp CC9605 Thermovirga lienii DSM 17291

46 bioRxiv preprint doi: https://doi.org/10.1101/001727; this version posted January 10, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SIANN: Strain Identification by Alignment to Near Neighbors

Thermus scotoductus SA 01 Vibrio parahaemolyticus RIMD Thermus sp CCB US3 UF1 2210633 Thermus thermophilus HB27 Vibrio sp EJY3 Thioalkalimicrobium cyclicum Vibrio splendidus LGP32 ALM1 Vibrio vulnificus CMCP6 Thioalkalivibrio sp K90mix Vulcanisaeta distributa DSM Thioalkalivibrio sulfidophilus HL 14429 EbGr7 Vulcanisaeta moutnovskia Thiobacillus denitrificans 768 28 ATCC 25259 Waddlia chondrophila WSU Thiomicrospira crunogena 86 1044 XCL 2 Weeksella virosa DSM 16922 Thiomonas intermedia K12 Weissella koreensis KACC Tolumonas auensis DSM 9187 15510 Treponema azotonutricium Wigglesworthia glossinidia ZAS 9 endosymbiont of Glossina Treponema brennaborense brevipalpis DSM 12168 Wolbachia endosymbiont of Treponema denticola ATCC Culex quinquefasciatus Pel 35405 Wolbachia sp wRi Treponema pallidum subsp Wolinella succinogenes DSM pallidum str Nichols 1740 Treponema paraluiscuniculi Xanthobacter autotrophicus Cuniculi A Py2 Treponema primitia ZAS 2 Xanthomonas albilineans GPE Treponema succinifaciens PC73 DSM 2489 Xanthomonas axonopodis pv Trichodesmium erythraeum citri str 306 IMS101 Xanthomonas campestris pv Tropheryma whipplei str Twist campestris str 8004 Truepera radiovictrix DSM Xanthomonas oryzae pv 17093 oryzae KACC 10331 Tsukamurella paurometabola Xenorhabdus bovienii SS 2004 DSM 20162 Xenorhabdus nematophila Ureaplasma parvum serovar 3 ATCC 19061 str ATCC 27815 Xylanimonas cellulosilytica Ureaplasma urealyticum DSM 15894 serovar 10 str ATCC 33699 Xylella fastidiosa 9a5c Variovorax paradoxus S110 Yersinia enterocolitica subsp Veillonella parvula DSM 2008 enterocolitica 8081 Verminephrobacter eiseniae Yersinia pestis CO92 EF01 2 Yersinia pseudotuberculosis IP Verrucosispora maris AB 18 32953 032 Zobellia galactanivorans Vibrio anguillarum 775 Zunongwangia profunda SM Vibrio cholerae O1 biovar El A87 Tor str N16961 Zymomonas mobilis subsp Vibrio fischeri ES114 mobilis ATCC 10988 Vibrio furnissii NCTC 11218 Vibrio harveyi ATCC BAA 1116

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