T-Coffee
Sign in to saveT-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from Protein Data Bank (PDB) files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by de
Key facts
- Software.name
- T-Coffee
- Software.developer
- Cédric Notredame, Centro de Regulacio Genomica (CRG) - Barcelona
- Software.latest release version
- 13.45.0.4846264
- Software.latest preview version
- 13.45.33.7d7e789
- Software.operating system
- Unix, Linux, Windows, macOS
- Software.genre
- Bioinformatics tool
- Software.licence
- GPL
via Wikipedia infobox
Source code
T-Coffee is a collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures. Note that the git repository is meant to support the packaging of new releases. If you simply want to install T-Coffee on your system please download the latest distribution from Clone the git repository on your computer with the following command: git clone [email protected]:cbcrg/tcoffee.git tcoffee make sure you have installed all dependencies cd tcoffee/t coffee/src make t coffee mv t coffee OR add current dir to your path - not recommended
Excerpt from the source-code README · 1,081 chars · not written by Vinony
Wikidata facts
- Official website
- tcoffee.org
Show 3 more facts
- source code repository URL
- github.com/cbcrg/tcoffee
- user manual URL
- tcoffee.readthedocs.io/en/latest
- software version identifier
- 12.00
via Wikidata · CC0
~6 min read
Article
9 sectionsContents
- Algorithm
- Generating a primary library of alignments
- Combination of the libraries
- Comparisons with other alignment software
- Variations
- Evaluation
- See also
- References
- External links
T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from Protein Data Bank (PDB) files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF, and FASTA format. The most common input formats are supported (FASTA, Protein Information Resource (PIR)).
==Algorithm== T-Coffee algorithm consist of two main features, the first by, using heterogeneous data sources, can provide simple and flexible means to generate multiple alignments. T-coffee can compute multiple alignments using a library that was generated using a mixture of local and global pair-wise alignments.