[ X ] Due to ongoing changes at NCBI, ProtoGene may experience technical problems in the coming days, till we fix all of them. https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/ http://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml

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
Expresso Aligns protein sequences using structural information   >>  Cite
PSI-Coffee Aligns distantly related proteins using homology extension (slow and accurate)   >>  Cite
Pro-Coffee Aligns homologous promoter regions (new)   >>  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

Core 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

Processing

ProtoGene Turning amino acid alignments into CDS nucleotide alignments   >>  Cite

Useful links

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

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
IGS CNRS  IGS lab., CNRS
>Max-Planck Institute Max-Planck Institute for Developmental Biology
Cornell Cornell
EMBNet-Spain EMBNet-Spain
CRG  Centre for Genomic Regulation (CRG)