[  etch  ] [  etch-m68k  ] [  lenny  ] [  squeeze  ] [  sid  ]
[ Source: t-coffee  ]

Package: t-coffee (8.14-1 and others)

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 also allows to 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: C, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Analysing, Comparing, Supports Format: Plain Text

Other Packages Related to t-coffee

  • depends
  • recommends
  • suggests
  • dep: libc0.1 (>= 2.7) [kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.10) [hurd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.10) [hppa]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.3) [mips]
    dep: libc6 (>= 2.5) [avr32]
    dep: libc6 (>= 2.5-5) [m68k]
    dep: libc6 (>= 2.7) [amd64, armel, i386, mipsel, powerpc, s390, sparc]
  • dep: libc6.1 (>= 2.7) [alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
  • sug: boxshade
    Pretty-printing of multiple sequence alignments
  • sug: clustalw
    global multiple nucleotide or peptide sequence alignment
  • sug: dialign-tx [not m68k]
    Segment-based multiple sequence alignment
  • sug: kalign
    Global and progressive multiple sequence alignment
  • sug: mafft
    Multiple alignment program for amino acid or nucleotide sequences
  • sug: muscle
    Multiple alignment program of protein sequences
  • sug: poa
    Partial Order Alignment for multiple sequence alignment
  • sug: probcons
    PROBabilistic CONSistency-based multiple sequence alignment
  • sug: seaview
    Multiplatform interface for sequence alignment and phylogeny
  • sug: t-coffee-doc
    PDF and HTML accompaning documents to T-Coffee
  • sug: t-coffee-examples
    annotated examples for the use of T-Coffee

Download t-coffee

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha 8.14-1 860.6 kB2124 kB [list of files]
amd64 8.14-1 723.5 kB1668 kB [list of files]
armel 8.14-1 679.8 kB1540 kB [list of files]
avr32 (unofficial port) 8.14-1 717.9 kB1364 kB [list of files]
hppa 8.14-1 741.3 kB1636 kB [list of files]
hurd-i386 8.14-1 652.1 kB1572 kB [list of files]
i386 8.14-1 652.3 kB1572 kB [list of files]
ia64 8.14-1 1,095.8 kB3200 kB [list of files]
kfreebsd-amd64 8.14-1 723.5 kB1662 kB [list of files]
kfreebsd-i386 8.14-1 652.0 kB1566 kB [list of files]
m68k (unofficial port) 5.72-1 434.8 kB1124 kB [list of files]
mips 8.14-1 745.1 kB2048 kB [list of files]
mipsel 8.14-1 747.5 kB2048 kB [list of files]
powerpc 8.14-1 732.6 kB1724 kB [list of files]
s390 8.14-1 705.1 kB1644 kB [list of files]
sparc 8.14-1 651.3 kB1548 kB [list of files]