Package: maffilter (1.3.1+dfsg-6 and others)

[ 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.

Other Packages Related to maffilter

• dep: libboost-iostreams1.83.0 (>= 1.83.0)

  Boost.Iostreams Library

• dep: libbpp-core4t64 (>= 2.4.1)

  Bio++ Core library

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

  Bio++ Phylogenetics library: genomics components

• dep: libbpp-phyl12t64 (>= 2.4.1)

  Bio++ Phylogenetic library

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

  Bio++ Sequence library: genomics components

• dep: libbpp-seq12t64 (>= 2.4.1)

  Bio++ Sequence library

• dep: libbz2-1.0 [sparc64]

  high-quality block-sorting file compressor library - runtime

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

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  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]

  library to determine the call-chain of a program - runtime

• dep: zlib1g (>= 1:1.1.4) [sparc64]

  compression library - runtime

• sug: maffilter-examples

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

Download maffilter

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.3.1+dfsg-6	240.8 kB	1,373.0 kB	[list of files]
amd64	1.3.1+dfsg-6	259.5 kB	1,308.0 kB	[list of files]
arm64	1.3.1+dfsg-6+b1	238.6 kB	1,369.0 kB	[list of files]
armel	1.3.1+dfsg-6	222.9 kB	1,179.0 kB	[list of files]
armhf	1.3.1+dfsg-6	228.8 kB	1,039.0 kB	[list of files]
hppa (unofficial port)	1.3.1+dfsg-6	248.4 kB	1,250.0 kB	[list of files]
i386	1.3.1+dfsg-6	266.2 kB	1,271.0 kB	[list of files]
ia64 (unofficial port)	1.3.1+dfsg-6	273.0 kB	1,911.0 kB	[list of files]
m68k (unofficial port)	1.3.1+dfsg-6	248.5 kB	1,255.0 kB	[list of files]
mips64el	1.3.1+dfsg-6	225.2 kB	1,489.0 kB	[list of files]
ppc64 (unofficial port)	1.3.1+dfsg-6	256.3 kB	1,560.0 kB	[list of files]
ppc64el	1.3.1+dfsg-6	254.5 kB	1,432.0 kB	[list of files]
riscv64	1.3.1+dfsg-6	248.2 kB	1,176.0 kB	[list of files]
s390x	1.3.1+dfsg-6	247.8 kB	1,320.0 kB	[list of files]
sh4 (unofficial port)	1.3.1+dfsg-6	284.3 kB	1,304.0 kB	[list of files]
sparc64 (unofficial port)	1.3.1+dfsg-6	220.7 kB	1,503.0 kB	[list of files]
x32 (unofficial port)	1.3.1+dfsg-6+b1	261.3 kB	1,252.0 kB	[list of files]