<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">A silly question here.</div><div class=""><br class=""></div><div class="">I am trying to get fast file in a genind form, easy. But the fast file contains 2 sequences per individual (diploid). I do not know how to set up the ploidy level; hence getting a genind object with two individuals rather than 4 (see below). </div><div class=""><br class=""></div><div class="">Fasta file looks like:</div><div class=""><br class=""></div><div class=""><div class="">>ind1-1</div><div class="">GACATGAGCAGCAACCTGCTGCGCCACGATGGAGCTGGCGTGCGGTGCCCGTGGGCTGAG</div><div class="">TCTCTGGCAGAGCTGGACCTGTCCTCCAATCAGTTGGCGGATGCTGTGTTTGAGTGCTTG</div><div class="">CCCGTCAACGTCAAAAAGCTCAGCCTAGAAAACAATCAGATCAGCAACGTGCCCAGGGGG</div><div class="">GTGGCGGAGCTGGAATCCTTGGAAGAGCTGAACCTGGCATCCAACAGGCTGGCTGACCTG</div><div class="">CCGGGGTGCAGCAGCTTTCCGTCCCTGCAGTTCCTGAACGCG</div><div class="">>ind1-2</div><div class="">GACATGAGCAGCAACCTGCTGCGCCACGATGGAGCTGGCGTGCGGTGCCCGTGGGCTGAG</div><div class="">TCTCTGGCAGAGCTGGACCTGTCCTCCAATCAGTTGGCGGATGCTGTGTTTGAGTGCTTG</div><div class="">CCCGTCAACGTCAAAAAGCTCAGCCTAGAAAACAATCAGATCAGCAACGTGCCCAGGGGG</div><div class="">GTGGCGGAGCTGGAATCCTTGGAAGAGCTGAACCTGGCATCGAACAGGCTGGCTGACCTG</div><div class="">CCGGGGTGCAGCAGCTTTCCGGCCCTGCAGTTCCTGAACGCG</div><div class="">>ind2-1</div><div class="">GACATGAGCAGCAACCTGCTGCGCCACGATGGAGCTGGCGTGCGGTGCCCGTGGGCTGAG</div><div class="">TCTCTGGCAGAGCTGGACCTGTCCTCCAATCAGTTGGCGGATGCTGTGTTTGAGTGCTTG</div><div class="">CCCGTCAACGTCAAAAAGCTCAGCCTAGAAAACAATCAGATCAGCAACGTGCCCAGGGGG</div><div class="">GTGGCAGAGCTGGAATCCTTGGAAGAGCTGAACCTGGCATCCAACAGGCTGGCTGACCTG</div><div class="">CCGGGGTGCAGCGGCTTTCCGGCCCTGCAGTTCCTGAACGCG</div><div class="">>ind2-2</div><div class="">GACATGAGCAGCAACCTGCTGCGCCACGATGGAGCTGGCGTGCGGTGCCCGTGGGCTGAG</div><div class="">TCTCTGGCAGAGCTGGACCTGTCCTCCAATCAGTTGGCGGATGCTGTGTTTGAGTGCTTG</div><div class="">CCCGTCAACGTCAAAAAGCTCAGCCTAGAAAACAATCAGATCAGCAACGTGCCCAGGGGG</div><div class="">GTGGCGGAGCTGGAATCCTTGGAAGAGCTGAACCTGGCATCCAA</div></div><div class=""><br class=""></div><div class="">Input as follow:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px 0px 0px 4px; text-indent: -4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class="">A</span></font><font color="#061a99" face="Monaco" class=""><span style="font-size: 11px;" class=""> <- read.dna(</span></font><font color="#b01600" face="Monaco" class=""><span style="font-size: 11px;" class="">“A.fas"</span></font><font color="#061a99" face="Monaco" class=""><span style="font-size: 11px;" class="">, </span></font><span style="color: rgb(0, 0, 0); font-family: Monaco; font-size: 11px;" class="">format</span><font color="#061a99" face="Monaco" class=""><span style="font-size: 11px;" class="">=</span></font><span style="color: rgb(176, 22, 0); font-family: Monaco; font-size: 11px;" class="">"fasta"</span><font color="#061a99" face="Monaco" class=""><span style="font-size: 11px;" class="">)</span></font></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; font-size: 11px; line-height: normal; font-family: Monaco;" class=""><span style="color: rgb(6, 26, 153);" class=""><span style="color: #000000" class="">A </span><- DNAbin2genind(</span>A<font color="#061a99" class="">)</font></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; font-size: 11px; line-height: normal; font-family: Monaco;" class="">A</div></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; font-size: 11px; line-height: normal; font-family: Monaco;" class=""><br class=""></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; line-height: normal;" class=""><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class="">/// GENIND OBJECT /////////</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> // 4 individuals; 4 loci; 8 alleles; size: 5.6 Kb</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> // Basic content</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @tab: 4 x 8 matrix of allele counts</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @loc.n.all: number of alleles per locus (range: 2-2)</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @loc.fac: locus factor for the 8 columns of @tab</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @all.names: list of allele names for each locus</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @ploidy: ploidy of each individual (range: 1-1)</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @type: codom</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> @call: DNAbin2genind(x = tlr)</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> // Optional content</span></font></div><div style="margin: 0px 0px 0px 4px; line-height: normal;" class=""><font face="Monaco" class=""><span style="font-size: 11px;" class=""> - empty -</span></font></div></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; font-size: 11px; line-height: normal; font-family: Monaco;" class=""><br class=""></div><div style="margin: 0px 0px 0px 4px; text-indent: -4px; font-size: 11px; line-height: normal; font-family: Monaco;" class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Carlos Lara</div><div class="">Dept of Zoology</div><div class="">University of Otago</div><div class="">New Zealand</div></body></html>