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