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mafft

Multiple alignment program for amino acid or nucleotide sequences

Variants:
MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm).
Homepage:
Package version:6.815-1
Architecture:i386
Distribution:Debian
Filename:mafft_6.815-1_i386.deb

/usr/share/doc/mafft/README.Debian

mafft for Debian
----------------

The mafft program is tested when we assemble our binary packages in our build
network. The following commands are run and compared to a reference output:

mafft                               test/sample | diff test/sample.fftns2 -
mafft --maxiterate 100              test/sample | diff test/sample.fftnsi -
mafft --globalpair                  test/sample | diff tes
more»

/usr/share/man/man1/mafft-homologs.1.gz

MAFFT-HOMOLOGS(1)           Mafft Manual           MAFFT-HOMOLOGS(1)



NAME
       mafft-homologs - aligns sequences together with homologues
       automatically collected from SwissProt via NCBI BLAST

SYNOPSIS
       mafft-homologs [options] input [> output]

DESCRIPTION
       The accuracy of an alignment of a few distantly related
       sequences is considerably improved when being aligned

more»

/usr/share/man/man1/mafft.1.gz

MAFFT(1)                    Mafft Manual                    MAFFT(1)



NAME
       mafft - Multiple alignment program for amino acid or
       nucleotide sequences

SYNOPSIS
       mafft [options] input [> output]

       linsi input [> output]

       ginsi input [> output]

       einsi input [> output]

       fftnsi input [> output]

       fftns input [> output]

       nwns input [> output]
more»

/usr/share/doc/mafft/changelog.Debian.gz

mafft (6.815-1) unstable; urgency=low

  * New upstream version
  * Switch to source format 3.0 (qui
more»

/usr/share/doc/mafft/copyright

Name    :  MAFFT
Contact :  Kazutaka Katoh <katoh@bioreg.kyushu-u.ac.jp>
Source  :  http://align.bmr
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