Dear biostars members,
I've multiple fasta files containing a different number of transcripts of different species (one file for each species). I want to find conserved regions in sequences between the species. I'm completely new to this topic. I've performed some search and I found ClustalW is suitable for such purpose. Other people use SEEKR and QuasiAlign. I've installed ClustalW but the command line requires only one input fasta file (-i argument). How can I feed the tool with multiple fasta files ?
Any idea about how to perform that, or can you provide me with tools and/or idea to do that?
Thanks in advance
Do you want just conserved regions, or gene orthologs? If you're interested in orthologs, you could use blast to find matches between each species and the other fasta files