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Paket: t-coffee (11.00.8cbe486-6)

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.

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  • dep: libstdc++6 (>= 4.1.1)
    GNU Standard C++ Library v3
  • 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
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    Segment-based multiple sequence alignment
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    Fast Statistical Alignment of protein, RNA or DNA sequences
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    multiple structural alignment of proteins
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    next generation suite of BLAST sequence search tools
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    Partial Order Alignment for multiple sequence alignment
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    Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
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    PROBabilistic CONSistency-based multiple sequence alignment
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    multiple alignment of protein sequences
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    structural alignment of proteins
  • sug: boxshade
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    annotated examples for the use of T-Coffee

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Arkitektur Paketstorlek Installerad storlek Filer
amd64 1.880,1 kbyte3687 kbyte [filförteckning]