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How to find the true orthologs from recipocal blast hits (blastn) ?

Hi,

After recipocal blast (blastn) analysis, from 7 different species, I got a ~10,000 orthologs as a final set. How do I find the true orthologs from the final set ?

Suggestions please!

Thanks

rna dna blast alignment
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written by sunnykevin97 sunnykevin97

Have you tried using databases of orthologous proteins like COG or EggNOG? The problem of assigning orthology groups is not simple at all.

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written by Asaf Asaf

Without phylogeny analysis there is a high error rate, but using MCL like OrthoMCL could probably help.

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written by Juke34 Juke34

Yes, I already did the analysis. Orthogroups_for_concatenated_alignment.txt file shows 1088 sequences. Can I consider these as orthologs ?

Or else, which folder/files do I consider the orthologs sequences ?

Thanks Kevin.

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written by sunnykevin97 sunnykevin97

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