Package: prime-phylo (1.0.11-11)

[ 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-mpi1.83.0 (>= 1.83.0)

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

• dep: libboost-serialization1.83.0 (>= 1.83.0)

  serialization library for C++

• dep: libc6 (>= 2.34)

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

• dep: libgcc-s1 (>= 3.5)

  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)

  high performance message passing library -- shared library

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

• 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

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