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…
Phytools
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Phytools Phylogenetic Tools for comparative biology

A multifunctional phylogenetics package. Phytools implements a number of…

A multifunctional phylogenetics package. Phytools implements a number of methods for phylogenetic comparative biology, phylogeny inference, tree manipulation and graphing. Its functionality is…

SURFACE
Desktop

SURFACE

A data-driven phylogenetic comparative method for fitting stabilizing selection…

A data-driven phylogenetic comparative method for fitting stabilizing selection models to continuous trait data, building on the ouch package. SURFACE consists of a ‘forward’ stepwise phase in…

Phangorn
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Phangorn

A package for phylogenetic reconstruction and analysis. Phangorn offers the…

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…

Diversitree
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Diversitree

A package which implements a series of methods for detecting associations…

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…

APE
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APE Analyses of Phylogenetics and Evolution

A package for use in molecular evolution and phylogenetics. APE provides both…

A package for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods…

Windex
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Windex

A package with which researchers can use the Wheatsheaf index to analyze…

A package with which researchers can use the Wheatsheaf index to analyze convergent evolution. Windex allows implementation of this method (the Wheatsheaf index) with additional functions that can be…

Phylocom
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Phylocom

A software for the analysis of phylogenetic community structure and character…

A software for the analysis of phylogenetic community structure and character evolution. Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within…

PHYREG
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PHYREG Phylogenetic Regression

A tool that implements the phylogenetic regression of Grafen. Phyreg provides…

A tool that implements the phylogenetic regression of Grafen. Phyreg provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and…

QueTAL
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QueTAL Que Transcription Activator-Like

Offers tailored tools for comparison of Transcripton Activation-Like (TAL)…

Offers tailored tools for comparison of Transcripton Activation-Like (TAL) effector genes to infer functional and evolutionary relationships. This toolkit contains two packages, DisTAL for distance…

COMPARE
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COMPARE

A tool for phylogenetic comparative methods. COMPARE analyzes interspecific…

A tool for phylogenetic comparative methods. COMPARE analyzes interspecific data in an evolutionary context. It applies several phylogenetic comparative methods (e.g., independent contrasts, spatial…

PHYSIG
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PHYSIG Phylogenetic Signal

A Matlab code for the phylogenetic analysis of comparative data using…

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…

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