Mcoffee help
Our implementation of Mcoffee
One of the most common situation when building multiple sequence alignments is to have several alignments produced by several alternative methods, and not knowing which one to choose. In this section, we show you that you can use M-Coffee to combine your many alignments into one single alignment. We show you here that you can either let T-Coffee compute all the multiple sequence alignments and combine them into one, or you can specify the methods you want to combine. M-Coffee is not always the best methods, but extensive benchmarks on BaliBase, Prefab and Homstrad have shown that it delivers the best alignment 2 times out of 3. If you do not want to use the methods provided by M-Coffee, you can also combine pre-computed alignments (see Mcoffee form -> 2.Multiple Methods ).
Notredame C, Higgins DG, Heringa J.T-Coffee: A novel method for fast and accurate multiple sequence alignment.J Mol Biol. 2000 Sep 8;302(1):205-17. PMID: 10964570 [PubMed - indexed for MEDLINE]
The official T_coffee web page is available at this link.
Mcoffee form
- Alignment Computation
- Pairwise Methods : Mcoffee computes its alignments by combining a collection of smaller alignments named a Library. You can choose pairwise and multiple sequence alignment methods
- Multiple Methods
| 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 |
| pcma | Profile Consistency Multiple sequence Alignment publication: reference |
| muscle | MUSCLE stands for multiple
sequence comparison by log-expectation publication: reference |
| dialignt |
DIALIGN-T is an improved algorithm for segment-based multiple protein
alignments publication: reference |
| poa | Multiple Sequence Alignment Using Partial Order Graphs publication: reference |
| clustalw | Clustalw can interact with t_coffee. publication:reference |
| tcoffee | homepage |
| mafft | MAFFT is a method for multiple sequence alignment based on fast Fourier transform publication: reference |
| probcons | Probabilistic Consistency-based Multiple Sequence Alignment publication: reference |
- Output
- You can choose the case and the look of results:
| Case |
upper |
upper case for residues |
| lower |
lower case for residues |
|
| Residue Number |
ON |
print residue number |
| OFF |
||
| Order |
input |
output order based on sequences input order |
| aligned | output order based on alignment |
Mcoffee Tutorials and Technical Notes
Please refer, to the T_coffee home page.T_coffee Tutorial (HTML) and T_coffee Technical Notes (HTML)