# T-Coffee ## A Tool For Multiple Sequence Alignments #### Notredame, Higgins, Heringa

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#### 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

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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 #### gapopen and gapext gapopen only no penalty | #### 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