Discrete trait evolution software tools | Phylogenomics data analysis
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 specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states.
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 its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.
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 family sizes, CAFE 3 provides a platform for expanding comparative genomic analyses into clades consisting solely of draft genome sequences.
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. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. The methods can be used to take into account uncertainty about the model of evolution and the underlying phylogeny. BayesTraits uses Markov chain Monte Carlo (MCMC) methods to derive posterior distributions and maximum likelihood (ML) methods to derive point estimates of, log-likelihoods, the parameters of statistical models, and the values of traits at ancestral nodes of phylogenies.
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 as a teaching tool for explaining stochastic models, Bayesian inference, and character histories. It has several types of function such as: (1) it calculates conditional likelihood for each character state at each node of the tree; or (2) it simulates ancestral states at each internal node by sampling from the posterior distribution of states.
Simulates the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. Seq-Gen has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of DNA sequence evolution. It also allows the repetitive simulation of DNA sequences under most of the models of nucleotide substitution that are commonly used for the reconstruction of phylogenies. Seq-Gen provides a flexible and efficient source of such simulations under a wide range of models of substitution, and may be a useful tool for researchers studying the phylogenetic relationships and molecular evolution of DNA sequences.
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 that reliably capture the underlying evolutionary processes. A variety of features are available including the ability to analyze the data with various evolutionary models, to infer gain and loss events using either stochastic mapping or maximum parsimony, and to estimate gain and loss rates for each character analyzed.
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 population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions.