Package: prime-phylo (1.0.11-13 and others)

[ Source: prime-phylo  ]

bayesian estimation of gene trees taking the species tree into account

PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees.

The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.

Other Packages Related to prime-phylo

• dep: libblas3

  Basic Linear Algebra Reference implementations, shared library

  or libblas.so.3

  virtual package provided by libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libboost-mpi1.74.0 (>= 1.74.0+ds1) [x32]

  C++ interface to the Message Passing Interface (MPI)

• dep: libboost-mpi1.83.0 (>= 1.83.0) [not x32]

  C++ interface to the Message Passing Interface (MPI)

• dep: libboost-serialization1.74.0 (>= 1.74.0+ds1) [x32]

  serialization library for C++

• dep: libboost-serialization1.83.0 (>= 1.83.0) [not x32]

  serialization library for C++

• dep: libc6 (>= 2.34) [hppa, m68k]

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

  dep: libc6 (>= 2.37) [sh4]

  dep: libc6 (>= 2.38) [not alpha, hppa, ia64, m68k, sh4]

• dep: libc6.1 (>= 2.37) [ia64]

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

  dep: libc6.1 (>= 2.38) [alpha]

• dep: libgcc-s1 (>= 3.0) [amd64, s390x, x32]

  GCC support library

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

  dep: libgcc-s1 (>= 3.4.4) [ppc64, ppc64el]

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

  dep: libgcc-s1 (>= 4.5) [arm64, mips64el, riscv64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: liblapack3

  Library of linear algebra routines 3 - shared version

  or liblapack.so.3

  virtual package provided by libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libopenmpi3t64 (>= 4.1.6) [hppa, ia64, m68k, sh4, x32]

  high performance message passing library -- shared library

• dep: libopenmpi40 (>= 5.0.6) [not hppa, ia64, m68k, sh4, x32]

  high performance message passing library -- shared library

• dep: libstdc++6 (>= 13.1) [hppa, ia64, m68k, sh4]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14) [not alpha, hppa, ia64, m68k, sh4]

  dep: libstdc++6 (>= 14.2.0-8) [alpha]

• dep: libunwind8 [ia64]

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

• dep: libxml2 (>= 2.7.4)

  GNOME XML library

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• sug: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• sug: mrbayes

  Bayesian Inference of Phylogeny

• sug: muscle

  Multiple alignment program of protein sequences

• sug: njplot

  phylogenetic tree drawing program

• sug: phyml

  Phylogenetic estimation using Maximum Likelihood

• sug: probalign

  multiple sequence alignment using partition function posterior probabilities

• sug: python3-biopython

  Python3 library for bioinformatics

• sug: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• sug: treeviewx

  Displays and prints phylogenetic trees

Download prime-phylo

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.0.11-13+b1	742.4 kB	3,598.0 kB	[list of files]
amd64	1.0.11-13+b1	825.4 kB	3,160.0 kB	[list of files]
arm64	1.0.11-13+b1	727.5 kB	3,319.0 kB	[list of files]
hppa (unofficial port)	1.0.11-11	818.0 kB	3,309.0 kB	[list of files]
ia64 (unofficial port)	1.0.11-11	892.6 kB	5,266.0 kB	[list of files]
m68k (unofficial port)	1.0.11-11	789.0 kB	2,992.0 kB	[list of files]
mips64el	1.0.11-13+b1	712.7 kB	3,703.0 kB	[list of files]
ppc64 (unofficial port)	1.0.11-13+b1	802.8 kB	4,088.0 kB	[list of files]
ppc64el	1.0.11-13+b1	808.5 kB	3,767.0 kB	[list of files]
riscv64	1.0.11-13+b1	794.1 kB	2,527.0 kB	[list of files]
s390x	1.0.11-13+b1	789.2 kB	3,159.0 kB	[list of files]
sh4 (unofficial port)	1.0.11-11	908.2 kB	3,255.0 kB	[list of files]
sparc64 (unofficial port)	1.0.11-13+b1	650.8 kB	13,513.0 kB	[list of files]
x32 (unofficial port)	1.0.11-12	842.2 kB	2,935.0 kB	[list of files]