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Can OrthoXML formats be used as input data of PosiGene? #7

Open ShuaiNIEgithub opened 4 years ago

ShuaiNIEgithub commented 4 years ago

Hello!

I am trying to run PosiGene and think it's great!

We know the OrthoMCL format is the output of arguably the most popular homology prediction software and of several databases of predicted homologs. Could you please tell me can PosiGene use OrthoMCL orthogroup as input file? And how to use it?

Thank you very much!

Shuai NIE

asahm commented 4 years ago

Dear Shuai NIE,

You can use the symbol based ortholog assignment to transfer the ortholog definition from another software to PosiGene. There is a chapter in the user guide about this topic. Briefly, you have to give in sequence-files which use the same gene IDs for orthologs across species. For fasta the format is >"sequence_ID|gene_ID". Make sure, however, that the sequence_IDs differ between the species.

Best, Arne