Package: maffilter (1.3.1+dfsg-6)

[ Source: maffilter  ]

process genome alignment in the Multiple Alignment Format

MafFilter applies a series of "filters" to a MAF file, in order to clean it, extract data and computer statistics while keeping track of the associated meta-data such as genome coordinates and quality scores.

 * It can process the alignment to remove low-quality / ambiguous /
   masked regions.
 * It can export data into a single or multiple alignment file in
   format such as Fasta or Clustal.
 * It can read annotation data in GFF or GTF format, and extract the
   corresponding alignment.
 * It can perform sliding windows calculations.
 * It can reconstruct phylogeny/genealogy along the genome alignment.
 * It can compute population genetics statistics, such as site
   frequency spectrum, number of fixed/polymorphic sites, etc.

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• dep: libboost-iostreams1.74.0 (>= 1.74.0+ds1) [x32]

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• dep: libboost-iostreams1.83.0 (>= 1.83.0) [not x32]

  Boost.Iostreams Library

• dep: libbpp-core4t64 (>= 2.4.1)

  Bio++ Core library

• dep: libbpp-phyl-omics3t64 (>= 2.4.1)

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• dep: libbpp-phyl12t64 (>= 2.4.1)

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• dep: libbpp-seq12t64 (>= 2.4.1)

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• dep: libbz2-1.0 [sparc64]

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• dep: libc6 (>= 2.34) [not alpha, ia64, sh4]

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• dep: libc6.1 (>= 2.34) [alpha]

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  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, i386, mips64el, ppc64, ppc64el, s390x, x32]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

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

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libstdc++6 (>= 13.1) [not alpha]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14-20240221-2.1) [alpha]

• dep: libunwind8 [ia64]

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• sug: maffilter-examples

  process genome alignment in the Multiple Alignment Format (example data)

Download maffilter

Download for all available architectures

Architecture	Package Size	Installed Size	Files
alpha (unofficial port)	240.8 kB	1,373.0 kB	[list of files]
amd64	259.5 kB	1,308.0 kB	[list of files]
arm64	237.9 kB	1,368.0 kB	[list of files]
armel	222.9 kB	1,179.0 kB	[list of files]
armhf	228.8 kB	1,039.0 kB	[list of files]
hppa (unofficial port)	248.4 kB	1,250.0 kB	[list of files]
i386	266.2 kB	1,271.0 kB	[list of files]
ia64 (unofficial port)	273.0 kB	1,911.0 kB	[list of files]
m68k (unofficial port)	248.5 kB	1,255.0 kB	[list of files]
mips64el	225.2 kB	1,489.0 kB	[list of files]
ppc64 (unofficial port)	256.3 kB	1,560.0 kB	[list of files]
ppc64el	254.5 kB	1,432.0 kB	[list of files]
riscv64	248.2 kB	1,176.0 kB	[list of files]
s390x	247.8 kB	1,320.0 kB	[list of files]
sh4 (unofficial port)	284.3 kB	1,304.0 kB	[list of files]
sparc64 (unofficial port)	220.7 kB	1,503.0 kB	[list of files]
x32 (unofficial port)	258.5 kB	1,251.0 kB	[list of files]