CEB Software
| Applications | top |
DIVA
| This program, authored by Fredrik Ronquist, implements a parsimony technique for reconstructing ancestral distributions of organisms known as Dispersal-Vicariance Analysis. The program has a command-line interface and is provided as executables for Macintosh and Windows machines at http://www.ebc.uu.se/systzoo/research/diva/diva.html. |
Migrate
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Migrate is a program to estimate population sizes and asymmetrical migration rates between populations and is authored by Peter Beerli. Migrate uses maximum likelihood and Bayesian approaches to analyze sequences (DNA, RNA), single nucleotide polymorphisms (SNP), microsatellites, and electrophoretic markers. Both approaches utilize the Metropolis-Hastings algorithm to integrate over all possible genealogical relationships. Future developments of Migrate include; speed improvements (via code optimization and additional parallelization) and the relaxation of some population genetic assumptions (e.g., the constancy of size and migration rates through time). Migrate runs on any modern computer platform and also runs on clusters using the Message Passing Interface. The C source code is distributed free of charge. Migrate homepage |
MrBayes
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MrBayes is a program for the Bayesian estimation of phylogeny and evolution. The current version is written by John Huelsenbeck (University of California, San Diego) and Fredrik Ronquist (Florida State University) but the next major release will be co-authored by Paul van der Mark (Florida State University), Bret Larget (University of Wisconsin, Madison), and Donald Simon (Duquesne University). MrBayes handles a wide variety of stochastic evolutionary models for molecular, morphological and other types of discrete data. It uses Metropolis-coupled Markov chain Monte Carlo techniques to estimate the posterior probability distribution. The program has a command-line interface and runs on all common platforms, including MPI-enabled cluster computers and shared-memory machines. The source code and executables are distributed free of charge from http://www.mrbayes.net. |
MrModeltest
| Mr. Modeltest is a program for performing hierarchical likelihood ratio tests and calculating approximate AIC and/or very approximate AICc values of the nucleotide substitution models currently implemented in both PAUP*4 and MrBayes v3. Version 2.2 also does some model averaging of the parameter estimates obtained by PAUP. MrModeltest 2.2 is a modified version of David Posada's Modeltest 3.6 (see Modeltest homepage). "Modified version" means that it was rewritten to compare 24 instead of 56 models of nucleotide substitution (basically a Modeltest version 1.0). On the other hand, all of the 24 models can be implemented in MrBayes version 3. Furthermore, MrModeltest uses (by default) four different hierarchies for the likelihood ratio tests. The hierarchies are described in detail in Posada, D. and K. A. Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology, 50:580-601 (Fig. 4a-d). download |
PAUP*
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PAUP*, written by David Swofford, infers phylogenetic trees from DNA and protein sequences and morphological data according to parsimony, distance, and maximum likelihood optimality criteria. In addition to tree-searching, PAUP* provides capabilities for data-format conversion, post-tree analyses such as consensus trees and ancestral-state reconstruction, and graphical output. PAUP* executables are available to run on Macintosh, Windows, Linux and several other Unix operating systems. Development versions of PAUP* support multithreading on multiprocessor machines and parallel computation on clusters and supercomputers, using MPI or PVM to distribute tree evaluations across processors. The program is sold and distributed by Sinauer and Associates, Inc. PAUP* homepage |
TreeFitter
| Written by Fredrik Ronquist, TreeFitter is a program for parsimony-based tree fitting. This is a technique that finds applications in gene tree - species tree fitting as well as in coevolutionary and biogeographic studies. TreeFitter has a command-line interface and implements some of the fastest algorithms known for parsimony-based tree fitting with horizontal transfer / host switches / dispersal events allowed. The user can fit single trees to each other, or reconstruct species trees / host trees / general area cladograms from large sets of gene trees / parasite trees / organism phylogenies. TreeFitter is provided as executables for Macintosh and Windows machines at http://www.ebc.uu.se/systzoo/research/treefitter/treefitter.html. |
| Scripts | top |
MrAIC
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MrAIC.pl is a Perl script for calculating AIC, AICc, BIC, and Akaike weights (for a review, see Burnham and Anderson, 2002) for nucleotide substitution models. Likelihood scores under different models are estimated using PHYML (Guindon and Gascuel, 2003). Input is DNA data in PHYML format (see below). If the argument -modeltest is parsed, 56 models (the ones tested in Modeltest [Posada and Crandall, 1998]) are evaluated in PHYML. Default is to test the 24 models that can be specified in MrBayes v3b5 (Ronquist and Huelsenbeck, 2003). These are JC, F81, K2P (aka K80), HKY, SYM and GTR, each combined with Propinv (I) and/or Gamma (G). A difference between Modeltest and MrAIC.pl is that MrAIC.pl does not evaluate all models on the same, approximate topology. Instead, PHYML is used to try to find the maximum of the likelihood function under all models. This is necessary for finding AIC, AICc, or BIC for the models. download |
RepMaker
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RepMaker by Jim Wilgenbusch is a simple perl utility for automatically making multiple NEXUS files. Files can be used to distribute a single PAUP* bootstrap analysis over multiple machines using the scheduler Condor or the perl utility BsLauncher (included with RepMaker). RepMaker is available free of charge on the web. Download |
mmml
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MMML by Jim Wilgenbusch is a simple perl program designed to facilitate mixed model maximum likelihood analysis (hence the name MMML). The primary analysis engine is PAUP*; therefore, PAUP* must be installed on your system and the binary must be in you path. The program uses the Parallel ForkManager perl model to take advantage of systems with multiple CPUs. The Parallel ForkManager is available for free at: http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm. download |
| Web Tools | top |
AWTY
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AWTY is a system for graphical exploration of Markov chain Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. The graphics produced by AWTY are designed to help assess whether an MCMC analysis has run long enough, such that tree topologies are being sampled in proportion to their true posterior probability distribution. In other words, "Are We There Yet?" or AWTY for short. AWTY homepage |
| Utilities | top |
Alignment Highlighting (vi)
| If you spend a lot of time using vi to edit your DNA sequence alignments you will probably find this extra by Johan Nylander useful. Add this to your directory to get color nucleotide symbols in the enhanced vi editor (vim). download |
NEXUS Syntax Highlighting (vi)
| If you spend a lot of time using vi to edit your NEXUS files you will probably find this extra by Johan Nylander useful. Add this to your directory to get syntax highlighting for the enhanced vi editor (vim). download |