How to use ClustalO?

[Joshua_HIT]

Nice to meet you all!

I want to extract a consensus transcriptome for 4 species. Now I have de novo assemblied all transcripts for 4 species. I want to use Clust-Omega to finish Multiple Sequences Alignment, but I can not find how to use Clust-Omega (I have installed in on my Linux by compliling source code).

I find this in clustalo --help:

clustalo -i my-in-seqs.fa -o my-out-seqs.fa -v

But it seems that only one .fasta can be inputed into program, but I have four. Does it means that I have to combined all fasta files together ? if it's so, I don't know how clusto will seperated each specie.

[krobison]

ClustalO is designed only for proteins; it really isn't an appropriate tool for transcriptomes unless you have found the ORFs and translated them.

Each file you give ClustalO would be one set of sequences to align to each other; ClustalO won't partition your sequences by family first. You need to do that, and then run the several thousand files (most of which will have 4 sequences -- one from each transcriptome), each as a ClustalO job.

[Joshua_HIT]

ClustalO is designed only for proteins; it really isn't an appropriate tool for transcriptomes unless you have found the ORFs and translated them.

Each file you give ClustalO would be one set of sequences to align to each other; ClustalO won't partition your sequences by family first. You need to do that, and then run the several thousand files (most of which will have 4 sequences -- one from each transcriptome), each as a ClustalO job.

Thank you so much ! I was a student of computer science, a totally freshman in Biology. it seems that I have been searching in wrong direction.

Thanks for your advise.