Package: t-coffee (12.00.7fb08c2-4)

[ Source: t-coffee  ]

Multiple Sequence Alignment

T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.

T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information

T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c, interface::commandline, Role: Program, Scope: Utility, Purpose: use::analysing, use::comparing, Supports Format: Need an extra tag, works-with-format::plaintext, works-with::TODO

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• dep: libgcc1 (>= 1:3.0) [not armhf]

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  dep: libgcc1 (>= 1:3.5) [armhf]

• dep: libstdc++6 (>= 4.1.1) [not armhf]

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  dep: libstdc++6 (>= 4.3.0) [armhf]

• rec: amap-align

  Protein multiple alignment by sequence annealing

• rec: clustalo

  General purpose multiple sequence alignment program for proteins

• rec: clustalw

  global multiple nucleotide or peptide sequence alignment

• rec: dialign-tx

  Segment-based multiple sequence alignment

• rec: fsa

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• rec: kalign

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• rec: libsoap-lite-perl

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• rec: libxml-simple-perl

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• rec: mafft

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• rec: muscle

  Multiple alignment program of protein sequences

• rec: mustang

  multiple structural alignment of proteins

• rec: ncbi-blast+

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• rec: poa

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• rec: prank

  Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

• rec: probcons

  PROBabilistic CONSistency-based multiple sequence alignment

• rec: proda

  multiple alignment of protein sequences

• rec: tm-align

  structural alignment of proteins

• sug: boxshade

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• sug: seaview

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• sug: t-coffee-examples

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Download t-coffee

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	1,484.5 kB	7,409.0 kB	[list of files]
arm64	1,384.2 kB	7,313.0 kB	[list of files]
armhf	1,352.9 kB	6,604.0 kB	[list of files]
i386	1,514.6 kB	7,761.0 kB	[list of files]