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Discrete trait evolution software tools | Phylogenomics

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to…
SimPhy
Desktop

SimPhy

A software package for the simulation of multiple gene families evolving under…

A software package for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to…

markophylo
Desktop

markophylo

Allows for fitting of maximum likelihood models using Markov chains on…

Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites,…

TestNH
Desktop

TestNH

Is dedicated to the testing of non-homogeneous process in sequence evolution.…

Is dedicated to the testing of non-homogeneous process in sequence evolution. TestNH provides a convenient and reliable approach where branches get clustered by their pattern of molecular evolution…

SIMMAP
Desktop

SIMMAP StochastIc Mutational MApping on Phylogenies

Serves for mapping character histories on phylogenies. SIMMAP uses a Bayesian…

Serves for mapping character histories on phylogenies. SIMMAP uses a Bayesian approach and enables researchers to address a wide variety of questions important in evolutionary studies. It can be used…

CAFE
Desktop

CAFE Computational Analysis of gene Family Evolution

Enables the accurate estimation of rates of gene family evolution when there…

Enables the accurate estimation of rates of gene family evolution when there are errors in the observed gene family sizes. By allowing users to marginalize over the uncertainty in the observed gene…

DupliPHY
Web

DupliPHY

A software tool to determine the evolutionary histories of gene families over a…

A software tool to determine the evolutionary histories of gene families over a phylogenetic tree. Given a set of gene family sizes and a phylogenetic tree DupliPHY will calculate the ancestral…

DupliPHY-ML
Desktop
Web

DupliPHY-ML

DupliPHY is a software tool to determine the evolutionary histories of gene…

DupliPHY is a software tool to determine the evolutionary histories of gene families using maximum likelihood. Given a set of gene family sizes and a phylogenetic tree DupliPHY-ML will calculate the…

SFREEMAP
Desktop

SFREEMAP

Provides an R-based implementation of an analytical approach to obtain…

Provides an R-based implementation of an analytical approach to obtain accurate, per-branch expectations of numbers of state transitions and dwelling times. SFREEMAP also introduces an intuitive way…

BayesTraits
Desktop

BayesTraits

A computer package for performing analyses of trait evolution among groups of…

A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available, these can be created using BayesPhylogenies.…

GLOOME
Desktop
Web

GLOOME Gain and Loss Mapping Engine

A user-friendly web server that accurately infers branch-specific and…

A user-friendly web server that accurately infers branch-specific and site-specific gain and loss events. The novel inference methodology is based on a stochastic mapping approach utilizing models…

Babel
Desktop

Babel

Allows users to model or explain data. Babel consists in an alternative model…

Allows users to model or explain data. Babel consists in an alternative model to the stochastic Dollo model. It can perform on cognate data for Transeurasian languages.

BadiRate
Desktop

BadiRate

A software tool to estimate family turnover rates, as well as the number of…

A software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. BadiRate implements two stochastic…

DiscML
Desktop

DiscML

Performs maximum likelihood estimation for evolutionary rates of discrete…

Performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior…

PhyloType
Web

PhyloType

Allows the reconstruction of ancestral traits and a number of criteria to…

Allows the reconstruction of ancestral traits and a number of criteria to select phylotypes. PhyloType is a web application permitting the analysis of phylogenies comprising several thousands of taxa…

Count
Desktop

Count

A software package for the analysis of numerical profiles on a phylogeny. It is…

A software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is…

BEGFE
Desktop

BEGFE Bayesian Estimation for Gene Family Evolution

A Bayesian method for estimating the evolutionary history of gene families.…

A Bayesian method for estimating the evolutionary history of gene families. BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and…

Mesquite
Desktop

Mesquite

A modular, extendible software tool for evolutionary biology, designed to help…

A modular, extendible software tool for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of…

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