T-Coffee A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures


T-Coffee Aligns DNA, RNA or Proteins using the default T-Coffee   >>  Cite
M-Coffee Aligns DNA, RNA or Proteins by combining the output of popular aligners   >>  Cite
R-Coffee Aligns RNA sequences using predicted secondary structures   >>  Cite
SARA-Coffee Aligns RNA sequences using tertiary structure   >>  Cite
Expresso Aligns protein sequences using structural information   >>  Cite
PSI-Coffee Aligns distantly related proteins using homology extension (slow and accurate)   >>  Cite
PSI/TM-Coffee Align Proteins using Homology Extension against Reduced Databases   >>  Cite
Pro-Coffee Aligns homologous promoter regions   >>  Cite
Accurate Automatically combine the most accurate modes for DNA, RNA and Proteins (experimental!)
Combine Combines two (or more) multiple sequence alignments into a single one   >>  Cite


TCS Evaluates your Alignment and outputs a Colored version indicating the local reliability.   >>  Cite
iRMSD-APDB Evaluates Multiple Sequence Alignment using structural information with APDB and iRMSD.   >>  Cite
T-RMSD Allows fine-grained structural clustering of a given group of related protein domains   >>  Cite
Strike Evaluation of protein MSAs using a single 3D structure   >>  Cite


Advanced Run your alignment using full featured T-Coffee options.   >>  Cite

Useful links

Google Group Support and discussion group
tcoffee.org Find out more about T-Coffee project and documentation
Cedric Notredame Home page, Courses and Blog
Download Sources and binaries are available for download at this link
Twitter Check it out for latest T-Coffee developments and new tips
Facebook T-Coffee has a page on Facebook
ResearchGate Follow the discussion on ResearchGate

Mirror sites

Bioinfo for dummies
The Book Bioinformatics For Dummies contains a T-Coffee tutorial and many other online resources.
Vital-IT Vital-IT, Swiss Institute of Bioinformatics (SIB)
EBI EBI, European Bioinformatics Institute
Max-Planck Institute Max-Planck Institute for Developmental Biology
Cornell Cornell
EMBNet-Spain EMBNet-Spain
Pasteur Institute Pasteur Institute