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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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Max character length for seq IDs #38

Closed Neato-Nick closed 3 years ago

Neato-Nick commented 3 years ago

VCF allows unlimited character length for sequence IDs, but apparently PHYLIP allows only 10. Would there be a way to force unique character names if the input is longer than 10 characters? Or, at least provide a warning that the output will be invalid?

Also, I got my vcf from graphtyper and the tool is working well!

edgardomortiz commented 3 years ago

I think I will add a warning when the names won't adhere to the Strict PHYLIP standard, however most current phylogenetic tools support Relaxed PHYLIP with no problem.

Thanks for the info about graphtyper, I will add it to the README and link it to this Issue

Neato-Nick commented 3 years ago

Ah ok, that makes sense. I'm new to this format, I ran into issues using SplitsTree

On Sat, Aug 14, 2021, 10:41 AM Edgardo M. Ortiz @.***> wrote:

I think I will add a warning when the names won't adhere to the Strict PHYLIP standard, however most current phylogenetic tools support Relaxed PHYLIP with no problem.

Thanks for the info about graphtyper, I will add it to the README and link it to this Issue

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