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edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GNU General Public License v3.0
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Using with Phylip #6

Closed mayasheth closed 5 years ago

mayasheth commented 6 years ago

Hi- what Phylip programs does this produce inputs for? I tried using the file with the Neighbor program and got an error that the input was of the wrong type.

Thanks!

edgardomortiz commented 6 years ago

Hello @mayasheth , In the README (https://github.com/edgardomortiz/vcf2phylip) I detail the output formats you can get. However I will specify that the PHYLIP format produced is the "relaxed" version. Honestly I never worked with the package PHYLIP, although they created the PHYLIP format (which is now used by many other phylogenetic programs). Reading the documentation of Phylip (http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles) I can tell the format my script produces is correct however there is a limitation for the strict Phylip format, the names of the samples must be exactly 10 characters long, you can try renaming your samples and running my script again. I could make my script to truncate the names to 10 characters but this may create non-unique names.

Let me know if this works.

Edgardo

edgardomortiz commented 5 years ago

Please re-open the issue if problem persists, closing this now.