A Bayesian Markov chain Monte Carlo (MCMC) program for analyzing DNA sequence alignments under the multispecies coalescent model (MSC). BPP analyses may include estimation of population size (theta's) and species divergence times (tau's), species tree estimation and species delimitation. BPP replaces the old program MCMCcoal.

User report

0 user reviews

0 user reviews

No review has been posted.

BPP forum

No open topic.

BPP classification

BPP specifications

Software type:
Package
Restrictions to use:
None
Input format:
PHYLIP/PAML
Output format:
TXT
Programming languages:
ANSI C
Version:
3.3
Source code URL:
http://abacus.gene.ucl.ac.uk/software/bpp3.3.tgz
Interface:
Command line interface
Input data:
A control file, a sequence alignment file, an Imap file
Output data:
Summary
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

Publications

BPP support

Documentation

Maintainer

Credits

Institution(s)

Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, UK

Funding source(s)

This study is supported by a grant from the Biotechnological and Biological Sciences Research Council (BBSRC).

Related Phylogenetic inference tools

Most Recent Tools

Desktop app
PolytomySolverNAD PolytomySolverNAD

PolytomySolverNAD

Is dedicated to the polytomy refinement problem. PolytomySolverNAD corrects a…

Is dedicated to the polytomy refinement problem. PolytomySolverNAD corrects a NAD (Non-Apparent Duplication) of the gene tree by applying multifurcation, given a rooted binary gene tree and species…

Desktop app
TreeTime TreeTime

TreeTime

Provides routines for ancestral sequence reconstruction and the inference of…

Provides routines for ancestral sequence reconstruction and the inference of molecular-clock phylogenies. TreeTime is a Markov chain Monte Carlo (MCMC) framework for Bayesian phylogeny…

Desktop app
phyloSkeleton phyloSkeleton

phyloSkeleton

Selects the most representative organisms, following a set of simple rules…

Selects the most representative organisms, following a set of simple rules based on taxonomy and assembly quality. phyloSkeleton allows users to retrieve the genomes from public databases (NCBI,…

Desktop app
FastTree FastTree

FastTree

Constructs large phylogenies and estimates their reliability. FastTree uses…

Constructs large phylogenies and estimates their reliability. FastTree uses nearest-neighbor interchanges (NNIs), the minimum-evolution criterion, minimum-evolution subtree-pruning-regrafting (SPRs)…

Most Popular Tools

PhyloPat PhyloPat

PhyloPat

Allows the complete Ensembl gene database to be queried using phylogenetic…

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.