PHYLIP file has not seq text.

I have a filtered vcf file with 9 wild dog genome samples..i want to run iqtree but when i try to convert my vcf2phylip with the commands

Phython vcf2phylip -i allsamples.vcf -o sample_1.vcf

The output file allsamples.vcf.min.phy has no seq.txt just the sample names..

Less allsamples.vcf.min.phy
~
~
~
~
~
~
~
~
9 0
Sample_1.bam
Sample_2.bam
Sample_3.bam
Sample_4.bam
Sample_5.bam
Sample_6.bam
Sample_7.bam
Sample_8.bam
Sample_9.bam

End...

Please help

iqtree alignment vcf vcf2phylip

• 1,045 views • link

updated 5.0 years ago by Gio12

• written 5.0 years ago by Kagisoralph •

1 answer

Without much description on what your python script looks like, I can't say what is going wrong. Have you considered using PGDSpider? That should be able to do your conversion.

• 0 views • link

written 5.0 years ago by Gio12

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