Package: t-coffee (13.41.0.28bdc39+dfsg-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

Other Packages Related to t-coffee

• dep: libc6 (>= 2.29)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.0) [not armel, armhf, ppc64el]

  GCC support library

  dep: libgcc-s1 (>= 3.4.4) [ppc64el]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

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

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 4.3.0) [armel, 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

  Fast Statistical Alignment of protein, RNA or DNA sequences

• rec: kalign

  Global and progressive multiple sequence alignment

• rec: libsoap-lite-perl

  Perl implementation of a SOAP client and server

• rec: libxml-simple-perl

  Perl module for reading and writing XML

• rec: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• rec: muscle

  Multiple alignment program of protein sequences

• rec: mustang

  multiple structural alignment of proteins

• rec: ncbi-blast+

  next generation suite of BLAST sequence search tools

• rec: poa

  Partial Order Alignment for multiple sequence alignment

• 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

  Pretty-printing of multiple sequence alignments

• sug: seaview

  Multiplatform interface for sequence alignment and phylogeny

• sug: t-coffee-examples

  annotated examples for the use of T-Coffee

Download t-coffee

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	979.6 kB	2,689.0 kB	[list of files]
arm64	879.1 kB	2,589.0 kB	[list of files]
armel	829.9 kB	2,504.0 kB	[list of files]
armhf	853.7 kB	1,912.0 kB	[list of files]
i386	998.4 kB	3,032.0 kB	[list of files]
mips64el	950.4 kB	3,335.0 kB	[list of files]
mipsel	935.9 kB	3,234.0 kB	[list of files]
ppc64el	1,031.5 kB	3,341.0 kB	[list of files]
s390x	898.0 kB	2,949.0 kB	[list of files]