PGDSpider version 2.1.1.2 (July 2017) An automated data conversion tool for connecting population genetics and genomics programs Author: Heidi Lischer Computational and Molecular Population Genetics lab (CMPG) Institute of Ecology and Evolution (IEE) University of Berne 3012 Bern Switzerland Member of the Swiss Institute of Bioinformatics (SIB) e-mail: [email protected] Download: http://cmpg.unibe.ch/software/PGDSpider/ Manual PGDSpider ver 2.1.1.2 19.07.2017 Contents 1 Introduction ......................................................................................................................... 4 2 Formats supported by PGDSpider ......................................................................................... 5 3 How to cite PGDSpider and License ....................................................................................... 8 4 System requirements ........................................................................................................... 8 5 Installing PGDSpider ............................................................................................................. 8 5.1 Installation Instructions ........................................................................................................... 8 5.2 Java Web Start ......................................................................................................................... 9 6 Execute PGDSpider GUI ...................................................................................................... 11 6.1 Increase memory ................................................................................................................... 11 6.2 How to use the PGDSpider GUI ............................................................................................. 11 6.3 SPID Editor ............................................................................................................................. 13 6.4 Menus .................................................................................................................................... 15 6.5 Shortcuts ............................................................................................................................... 17 6.6 Log Output ............................................................................................................................. 19 7 Execute PGDSpider-cli ........................................................................................................ 20 7.1 Examples ................................................................................................................................ 21 8 Conversion examples ......................................................................................................... 22 9 Reporting bugs and comments ........................................................................................... 23 10 File format descriptions and PGDSpider questions .............................................................. 24 10.1 PGD ........................................................................................................................................ 26 10.2 ARLEQUIN .............................................................................................................................. 38 10.3 BAM ....................................................................................................................................... 44 10.4 BAMOVA ................................................................................................................................ 46 10.5 BAPS....................................................................................................................................... 49 10.6 BATWING ............................................................................................................................... 55 10.7 Bayenv ................................................................................................................................... 57 10.8 BCF ......................................................................................................................................... 59 10.9 CONVERT ............................................................................................................................... 62 10.10 EIGENSOFT ......................................................................................................................... 64 10.11 FASTA ................................................................................................................................. 67 10.12 Extended multi-FASTA (XMFA) .......................................................................................... 70 Heidi Lischer page 2/178 Manual PGDSpider ver 2.1.1.2 19.07.2017 10.13 FASTQ ................................................................................................................................ 72 10.14 FDist2 ................................................................................................................................. 74 10.15 FSTAT ................................................................................................................................. 76 10.16 GDA .................................................................................................................................... 79 10.17 GENELAND ......................................................................................................................... 83 10.18 GENEPOP ........................................................................................................................... 87 10.19 GENETIX ............................................................................................................................. 90 10.20 GESTE / BayeScan .............................................................................................................. 93 10.21 HGDP ................................................................................................................................. 95 10.22 HGDP-CEPH ........................................................................................................................ 97 10.23 Immanc and BayesAss ....................................................................................................... 98 10.24 IM/IMa ............................................................................................................................. 101 10.25 IMa2 ................................................................................................................................. 104 10.26 KML .................................................................................................................................. 108 10.27 MAF ................................................................................................................................. 110 10.28 MEGA ............................................................................................................................... 115 10.29 MIGRATE .......................................................................................................................... 120 10.30 MSA ................................................................................................................................. 127 10.31 MSVar .............................................................................................................................. 129 10.32 NewHybrids ..................................................................................................................... 131 10.33 NEXUS .............................................................................................................................. 134 10.34 ONeSAMP ........................................................................................................................ 141 10.35 PED .................................................................................................................................. 143 10.36 PHYLIP .............................................................................................................................. 146 10.37 SAM ................................................................................................................................. 151 10.39 Structurama ..................................................................................................................... 156 10.40 STRUCTURE (fastSTRUCTURE) ......................................................................................... 158 10.41 VCF ................................................................................................................................... 163 11 PGDSpider Screenshots ..................................................................................................... 171 12 References (Literature) ...................................................................................................... 176 Heidi Lischer page 3/178 Manual PGDSpider ver 2.1.1.2 19.07.2017 1 Introduction PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs (Fig. 1) for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly