finding orthologous genes from multiple transcriptomes

Question

[majeedaasim]

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

Answer 1

[h.mon]

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.