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jydu / maffilter

The MafFilter genome alignment processor
GNU General Public License v3.0
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phylip format filter #17

Closed yywyaoyaowu closed 2 years ago

yywyaoyaowu commented 2 years ago

Hi I tried to use mafFilter to filter out the alignment with fewer 3 species. While I don't have the maf format input, I only have the phlip format. Do you have any tools for phylip format filter? Or anytools that can transfer phylip into maf? Thanks very much! Yao

jydu commented 2 years ago

Dear Yao,

MafFilter cannot read a file in phylip format, as this format does not permit to encode synteny breaks for instance. I am not aware of any converter... I once had to convert a fasta file generated by a simulator (so no synteny break, just SNPs), and I made a script with biopython for that purpose.

Best,

Julien.