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finding orthologous genes from multiple transcriptomes

I have RNAseq data of 16 species and I want to analyse the phylogenetic relation between them. For this I need to identify the orthologous genes between them to construct phylogenetic tree. Many tools are available for doing this. They require to perform BLAST analysis first. I need to know how to blast my 16 transcriptomes, Do I need to BLAST them against each other or against any other database as is evident from the literature.

Thanks

rna-seq orthologous genes blast
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updated by h.mon h.mon • written by majeedaasim • majeedaasim

1 answer

You should choose a program / algorithm based on careful reading of the literature, then read its manual and paper to learn its requirements.

The software I know (e.g. OrthoMCL, Proteinortho) use an all-vs-all blast, that is, each species blasted against species.

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written by h.mon h.mon

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