The use of phylogenetic comparative methods in evolutionary biology has seen a remarkable increase in recent years. Much of this growth has resulted from the proliferation of newly developed methods and a shift toward implementation of these methods in R, which has enhanced the flexibility and between-method compatibility of their implementation. Convergent evolution, or the independent evolution of similar phenotypes, is a commonly observed phenomenon across the tree of life.
A multifunctional phylogenetics package. Phytools implements a number of methods for phylogenetic comparative biology, phylogeny inference, tree manipulation and graphing. Its functionality is concentrated in the phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian and ML (maximum likelihood) ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple Brownian rates and correlations; visualizing discrete and continuous character evolution using colors or projections into trait space; identifying the location of a change in the rate of character evolution on the tree, etc.
A package for phylogenetic reconstruction and analysis. Phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, it provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.
Provides resource for data analysis, data management, and graphics. Stata is an integrated statistical software package where all analyses can be reproduced and documented for publication and review. User can combine and reshape datasets, manage variables, and collect statistics across groups or replicates. It also has advanced tools for managing specialized data such as survival/duration data, time-series data, panel/longitudinal data, multilevel data, categorical data, multiple-imputation data, and survey data.
Provides a package for use in molecular evolution and phylogenetics. APE supplies both utility functions for reading and writing data, manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis. It focuses on statistical analyses using phylogenetic and genealogical trees as input. It also produces complex population genetics plots, such as the generalized skyline plot and supports big data and quality check (QC).
A Matlab code for the phylogenetic analysis of comparative data using Generalized Least Squares and computer-intensive methods. Physig will perform the randomization test for phylogenetic signal and also calculate the K statistic to gauge how much phylogenetic signal is present. It tests for statistical significance of phylogenetic signal (tendency for related species to resemble each other) by randomization procedure, computes K statistic, which indicates amount of phylogenetic signal relative to expectation under Brownian motion character evolution along the specified phylogenetic tree (topology plus branch lengths. Physig also computes other MSE statistics.
A software for the analysis of phylogenetic community structure and character evolution. Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.
A package which implements a series of methods for detecting associations between species traits and rates of speciation and/or extinction, given a phylogeny and trait data, including the BiSSE (binary state speciation and extinction) method. Diversitree is open source and designed to be fairly straightforward to extend. In particular, any model that can be expressed by moving down a tree (post-order traversal, or ‘pruning’) can be implemented using only a modest number of lines of R code. To facilitate the development of related methods, there is a ‘writing diversitree extensions’ manual available from the diversitree website.