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

Alignment

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

Evaluation

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

Other

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, Swiss Institute of Bioinformatics (SIB)
	EBI, European Bioinformatics Institute
	IGS lab., CNRS
	Max-Planck Institute for Developmental Biology
	Cornell
	EMBNet-Spain
	Pasteur Institute