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T-Coffee (version 13.45.0.4846264)

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