What it does
This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs.
This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.
The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ .
Example
Suppose you have 5 sequences in FASTA format:
>1aboA NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS NYITPVN >1ycsB KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY VPRNLLGLYP >1pht GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG WLNGYNETTGERGDFPGTYVEYIGRKKISP >1vie DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI N >1ihvA NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD
By selecting "Yes" in output fasta_aln in the wrapper, the user will obtain the multiple alignment in FASTA format:
>1aboA NL-FVA---LYDFVASGDNTLSITKGEKLR-------VLGYN-------H NGEWCEA--QTKN-GQGWVPSNYIT------PVN >1ycsB KGVIYA---LWDYEPQNDDELPMKEGDCMT-------IIHREDE-----D EIEWWWA--RLND-KEGYVPRNLLG------LYP >1pht GYQYRA---LYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPE EIGWLNGYNETTG-ERGDFPGTYVEYIGRKKISP >1vie DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------ ------S--EAHPGSVQIYPVAALE------RIN >1ihvA NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S DI--------------KVVPRRKAK-----IIRD