BSD Ports

biology/mafft 7.267_1 FreeBSD

Multiple alignment program for amino acid or nucleotide sequences

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
BSD2CLAUSE
Categories
biology
Package size
903.5 KiB, 8683.6 KiB installed

Description

MAFFT offers a range of multiple alignment strategies, L-INS-i (accurate; recommended for <200 sequences), FFT-NS-i (standard speed and accuracy), FFT-NS-2 (fast; recommended for >2,000 sequences), etc. According to BAliBASE and other benchmark tests, L-INS-i is one of the most accurate methods currently available.

MAFFT has been described:

K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298) Recent developments in the MAFFT multiple sequence alignment program.

K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30: 3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

In the other systems

SystemPortVersion
FreeBSDbiology/mafft7.267_1
DragonFlybiology/mafft7.267_1
HardenedBSDbiology/mafft7.267_1
GhostBSDbiology/mafft7.267_1

Install

Binary package:

pkg install mafft

From the ports tree:

cd /usr/ports/biology/mafft/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	mafft>0:biology/mafft

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest7.267_17.267_17.2677.267_17.267_1
FreeBSD:14:quarterly7.267_17.267_1n/a7.267_17.267_1
FreeBSD:15:latest7.267_17.267_1n/a7.267_17.267_1
FreeBSD:15:quarterly7.267_17.267_1n/an/an/a
FreeBSD:16:latest7.267_17.267_1n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 3
Required by 1

Configuration

Options name: biology_mafft

OptionDefaultDescription
DOCSoffBuild and/or install documentation
EXAMPLESoffBuild and/or install examples
USES
gmake shebangfix tar:tgz
Service scripts
none

Files

Manual pages 2
  • mafft(1)
  • mafft-homologs(1)
pkg-plist 67
  • bin/einsi
  • bin/fftns
  • bin/fftnsi
  • bin/ginsi
  • bin/linsi
  • bin/mafft
  • bin/mafft-distance
  • bin/mafft-einsi
  • bin/mafft-fftns
  • bin/mafft-fftnsi
  • bin/mafft-ginsi
  • bin/mafft-homologs.rb
  • bin/mafft-linsi
  • bin/mafft-nwns
  • bin/mafft-nwnsi
  • bin/mafft-profile
  • bin/mafft-qinsi
  • bin/mafft-xinsi
  • bin/nwns
  • bin/nwnsi
  • libexec/mafft/addsingle
  • libexec/mafft/contrafoldwrap
  • libexec/mafft/countlen
  • libexec/mafft/disttbfast
  • libexec/mafft/dndblast
  • libexec/mafft/dndfast7
  • libexec/mafft/dndpre
  • libexec/mafft/dvtditr
  • libexec/mafft/f2cl
  • libexec/mafft/getlag
  • libexec/mafft/mafft-distance
  • libexec/mafft/mafft-profile
  • libexec/mafft/mafftash_premafft.pl
  • libexec/mafft/makedirectionlist
  • libexec/mafft/mccaskillwrap
  • libexec/mafft/multi2hat3s
  • libexec/mafft/pair2hat3s
  • libexec/mafft/pairash
  • libexec/mafft/pairlocalalign
  • libexec/mafft/regtable2seq
  • libexec/mafft/replaceu
  • libexec/mafft/restoreu
  • libexec/mafft/score
  • libexec/mafft/seekquencer_premafft.pl
  • libexec/mafft/seq2regtable
  • libexec/mafft/setcore
  • libexec/mafft/setdirection
  • libexec/mafft/sextet5
  • libexec/mafft/splittbfast
  • libexec/mafft/tbfast
  • libexec/mafft/version
  • share/man/man1/mafft-homologs.1.gz
  • share/man/man1/mafft.1.gz
  • share/doc/mafft/readme
  • share/examples/mafft/sample
  • share/examples/mafft/sample.dpparttree
  • share/examples/mafft/sample.fftns2
  • share/examples/mafft/sample.fftnsi
  • share/examples/mafft/sample.gins1
  • share/examples/mafft/sample.ginsi
  • share/examples/mafft/sample.ginsi.allowshift
  • share/examples/mafft/sample.lins1
  • share/examples/mafft/sample.linsi
  • share/examples/mafft/sample.parttree
  • share/examples/mafft/samplerna
  • share/examples/mafft/samplerna.qinsi
  • share/examples/mafft/samplerna.xinsi
distinfo 1
FileSizeSHA256
mafft-7.267-without-extensions-src.tgz43517460526e38d3faf3e8d96d9a2e2ecfc9662f0e61c71ed2bc35d07c769703ee86f6
Master sites 1
  • http://mafft.cbrc.jp/alignment/software/

Commit history 0

No commits in the history this site was built from.