Package: prank (0.0.170427+dfsg-3 and others)

[ Source: prank  ]

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

PRANK is a command-line program for UNIX-style environments but the same sequence alignment engine is implemented in the graphical program PRANKSTER. In addition to providing a user-friendly interface to those not familiar with Unix systems, PRANKSTER is an alignment browser for alignments saved in the HSAML format. The novel format allows for storing all the information generated by the aligner and the alignment browser is a convenient way to analyse and manipulate the data.

PRANK aims at an evolutionarily correct sequence alignment and often the result looks different from ones generated with other alignment methods. There are, however, cases where the different look is caused by violations of the method's assumptions. To understand why things may go wrong and how to avoid that, read this explanation of differences between PRANK and traditional progressive alignment methods.

Other Packages Related to prank

• dep: libc6 (>= 2.29) [not alpha, ia64, riscv64, sh4]

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

  dep: libc6 (>= 2.31) [sh4]

  dep: libc6 (>= 2.34) [riscv64]

• dep: libc6.1 (>= 2.29) [alpha]

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

  dep: libc6.1 (>= 2.31) [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) [riscv64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 5.2) [armel, armhf]

  dep: libstdc++6 (>= 9) [not armel, armhf, riscv64]

• dep: libunwind8 [ia64]

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

• enh: t-coffee

  Multiple Sequence Alignment

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Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	0.0.170427+dfsg-3	357.3 kB	1,481.0 kB	[list of files]
amd64	0.0.170427+dfsg-3	386.0 kB	1,180.0 kB	[list of files]
arm64	0.0.170427+dfsg-3	318.8 kB	1,044.0 kB	[list of files]
armel	0.0.170427+dfsg-3	328.1 kB	1,091.0 kB	[list of files]
armhf	0.0.170427+dfsg-3	333.8 kB	779.0 kB	[list of files]
hppa (unofficial port)	0.0.170427+dfsg-3	372.5 kB	1,200.0 kB	[list of files]
i386	0.0.170427+dfsg-3	395.6 kB	1,303.0 kB	[list of files]
ia64 (unofficial port)	0.0.170427+dfsg-3	454.4 kB	2,721.0 kB	[list of files]
m68k (unofficial port)	0.0.170427+dfsg-3	371.7 kB	1,351.0 kB	[list of files]
mips64el	0.0.170427+dfsg-3	309.6 kB	1,335.0 kB	[list of files]
ppc64 (unofficial port)	0.0.170427+dfsg-3	342.6 kB	1,384.0 kB	[list of files]
ppc64el	0.0.170427+dfsg-3	349.3 kB	1,320.0 kB	[list of files]
riscv64	0.0.170427+dfsg-3+b1	373.2 kB	885.0 kB	[list of files]
s390x	0.0.170427+dfsg-3	336.6 kB	1,188.0 kB	[list of files]
sh4 (unofficial port)	0.0.170427+dfsg-3	459.6 kB	1,100.0 kB	[list of files]
sparc64 (unofficial port)	0.0.170427+dfsg-3	306.1 kB	1,164.0 kB	[list of files]
x32 (unofficial port)	0.0.170427+dfsg-3	386.7 kB	1,151.0 kB	[list of files]