T_coffee help
Our web implementation of T_coffee
Installed T_coffee
We have currently installed version 5.0.3 of the T_coffee.The reference for this tool is:
The official T_coffee web page is available at this link.
T_coffee form
- Alignment Computation
- Pairwise Methods : Tcoffee computes its alignments by combining a collection of smaller alignments named a Library. In this section you can select the methods you want to combine into the Tcoffee library. You can choose pairwise and multiple sequence alignment methods
- Output
- You can choose the case and the look of results:
| modality | fast | Makes a global fasta style pairwise alignment. For proteins, matrix=blosum62mt, gep=-1, gop=-10, ktup=2. For DNA, matrix=idmat (id=10), gep=-1, gop=-20, ktup=5. Each pair of residue is given a score function of the weighting mode defined by -weight. |
| slow | Slow_pair : Identical to fast_pair, but does a full dynamic programming, using the myers and miller algorithm. This method is recommended if your sequences are distantly related. | |
| |
lalign | produces local alignments |
| |
clustalw | Uses clustalw (default parameters) to align two sequences. Each pair
of residue is given a score function of the weighting mode defined by -weight.e |
| Case |
upper |
upper case for residues |
| lower |
lower case for residues |
|
| Residue Number |
ON |
print residue number |
| OFF |
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| Order |
input |
output order based on sequences input order |
| aligned | output order based on alignment |
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T_coffee Tutorials and Technical Notes
Please refer, to the T_coffee home page.T_coffee Tutorial (HTML) and T_coffee Techmical Notes (HTML)