Hi
I work with non-model organisms trying to understand the orthologs transcripts shared among the different species.
I de novo assembled the transcripts using TRINITY
Removed redundant transcripts using CDHIT
How to find the orthologs common among the species , is their any tools of interest that can do the job ?
Suggestions please.
Thanks Kevin
Predicted ORF's using Transdecoder. Subjected the aminoacid sequences of each species into Orthofinder. I generated comparative stats about the shared orthologs among all species. How do I extract Orthology sequences ? further doing MSA alignment -> positive selection analysis (dN/dS).
Suggestions please!
What do you mean by "orthology sequences", consensus sequences?
Answers please! :D
The sequences shared among the all the nine species in my case.
I generated the alignment by performing multiple sequence alignment.