how to find ortholog genes in assembled transcriptome and make phylogenetic tree with close taxonomic groups

Question

[Mehmet]

Dear All,

I have an assembled and functionally annotated transcriptome data of a species. I want to find ortholog genes in the data and to make a phylogenetic tree with another species in different taxonomic group. what should the workflow be to find orthologs? Can you give advise ?

Thanks

[Prakki Rama]

check this post for finding orthologus genes. To make a phylogenetic tree, you have to use MSA tools like MEGA or CLUSTALX and find the phylogenetic relationship.

Answer 1

[h.mon]

You may use the Agalma pipeline. You may start from the very beginning (using Agalma to assemble your transcriptomes, find orthologous and reconstruct a phylogeny), or insert your data in any step along the way. Check its publication for an overview.

[Mehmet]

Hi,

Thank you very much for your help. I have already assembled my transcriptome data of a species, and now I want to find orthologous in my assembly and other closely related species, then to make a phylogenetic tree. I am trying to install Agalma to my supercomputer account. Could you help me in any step of my work when I ask?