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T-Coffee: A Consistency Based Multiple Alignmnent Method Multiple Alignments (Notredame,Higgins, Heringa)

T-Coffee

A Tool For Multiple Sequence Alignments

Notredame, Higgins, Heringa

T-Coffee will combine together several alignments. By default, T-Coffee will generate the 20 best local alignments (lalign) and the best global alignment for each pair of sequences. It will then combine all this information into one multiple sequence alignment. If you request it (Methods), T-Coffee can also generate and combine several multiple alignments using the most common methods (prrp, pima, dialign...), or use your own multiple sequence alignmnents (Data Input).

For a default utilisation, simply paste or upload your sequences in the box 1 on Data Input and press the run button (Limit: 20 sequences 300 residues)

Labelling

Type in the name of your alignment
Your e-mail
Results

Data Input

Sequences, Alignments or Libraries

In each field, input either a set of sequences, a multiple alignment or a library. All the fields do not need to be to be filled.

1

input a File Name or Paste

2

input a file Name or Paste

3

input a file Name or Paste

4

input a file Name or Paste

5

input a file Name or Paste

Data Output

Check the format you wish to produce

Alignment Format

msf

clustalw

fasta

color (html)

color (ps)

color (pdf)

Methods

Check the methods you wish to use

Substitution Matrix

 WARNING: if you select a matrix, NO OTHER method will be used

Pairwise Methods

lalign(pair)

clustalw(pair)

fast(pair)

checked fast(pair)

 

 

Multiple Aln Methods

clustalw

prrp

 

Extended Parameters

Multiple Aln

gapopen

gapext

cosmetic penalty

terminal gap

dp mode

normalise

your tree

tree computation

  

Fasta_pair_wise

ktuple

ndiag

diag evaluation

similarity matrix

    

Output

output order

Residue Number

Case

This page was produced by Cedric Notredame (Cedric.notredame@europe.com)

Please do not hesitate to send me any feed back you may feel appropriate