Package ‘seqinr’ June 9, 2021 Encoding UTF-8 Version 4.2-8 Date 2021-05-18 Title Biological Sequences Retrieval and Analysis Author Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Nec¸sulea[ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb] Maintainer Simon Penel <[email protected]> BugReports http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum Imports ade4,segmented Depends R (>= 2.10.0) Description Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>. License GPL (>= 2) SystemRequirements zlib headers and library. URL http://seqinr.r-forge.r-project.org/ NeedsCompilation yes Repository CRAN Repository/R-Forge/Project seqinr Repository/R-Forge/Revision 2130 Repository/R-Forge/DateTimeStamp 2021-05-25 12:22:25 Date/Publication 2021-06-09 04:20:02 UTC 1 2 R topics documented: R topics documented: seqinr-package . .5 a...............................................5 aaa..............................................6 aacost . .8 aaindex . 10 AAstat . 23 acnucopen . 24 al2bp . 26 alllistranks . 27 amb ............................................. 28 AnoukResult . 30 as.alignment . 30 as.matrix.alignment . 31 autosocket . 32 baselineabif . 33 bma ............................................. 34 c2s.............................................. 35 cai.............................................. 36 caitab . 38 chargaff........................................... 39 choosebank . 42 circle . 44 closebank . 45 clustal . 46 col2alpha . 47 comp ............................................ 48 computePI . 49 consensus . 50 count . 52 countfreelists . 54 countsubseqs . 56 crelistfromclientdata . 57 dia.bactgensize . 59 dinucl . 60 dinucleotides . 62 dist.alignment . 64 dotchart.uco . 65 dotPlot . 66 draw.oriloc . 68 draw.rearranged.oriloc . 70 draw.recstat . 71 ec999 . 72 ECH............................................. 73 EXP............................................. 74 extract.breakpoints . 77 extractseqs . 78 R topics documented: 3 fasta............................................. 80 fastacc . 81 G+C Content . 85 gb2fasta . 89 gbk2g2 . 90 gbk2g2.euk . 91 gcO2............................................. 92 gcT ............................................. 93 get.db.growth . 94 getAnnot . 96 getFrag . 97 getKeyword . 99 getLength . 100 getlistrank . 101 getliststate . 102 getLocation . 104 getName . 105 getSequence . 106 getTrans . 108 getType . 111 gfrag . 112 ghelp . 113 gs500liz . 114 identifiler . 115 isenum . 116 JLO ............................................. 117 kaks............................................. 118 kaksTorture . 121 knowndbs . 122 lseqinr . 124 m16j............................................. 124 mase............................................. 126 modifylist . 127 move............................................. 129 msf ............................................. 130 n2s.............................................. 131 oriloc . 132 parser.socket . 135 peakabif . 136 permutation . 137 phylip . 139 pK.............................................. 139 plot.SeqAcnucWeb . 141 plotabif . 142 plotladder . 144 plotPanels . 145 pmw............................................. 146 prepgetannots . 148 4 R topics documented: prettyseq . 149 print.qaw . 150 print.SeqAcnucWeb . 151 prochlo . 152 query . 154 read.abif . 157 read.alignment . ..