• phytools

  • Referenced in 13 articles [sw10003]
  • ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple ... discrete and continuous character evolution using colors or projections into trait space; identifying the location ... change in the rate of character evolution on the tree; fast Brownian motion simulation ... under several other models of continuous trait evolution; fitting a model of correlated binary trait...
  • diversitree

  • Referenced in 6 articles [sw26122]
  • mostly focusing on analysing diversification and character evolution. Contains implementations of ’BiSSE’ (Binary State ’Speciation ... Markov models of discrete and continuous trait evolution and constant rate ’speciation’ and extinction...
  • mvMORPH

  • Referenced in 4 articles [sw20088]
  • Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series...
  • Picante

  • Referenced in 5 articles [sw08306]
  • Phylocom integration, community analyses, null-models, traits and evolution...
  • OUOUCIR

  • Referenced in 1 article [sw34465]
  • Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation ... have been widely used to study trait evolution. In particular, two members of Gaussian processes ... been frequently applied for describing continuous trait evolution. Several models (OUBM, OUOU, OUBMBM, OUOUBM) have ... other traits. Applying the Cox-Ingersoll-Ross (CIR) process on rate of evolution, which prevents...
  • Treevo

  • Referenced in 1 article [sw32289]
  • doing phylogenetic comparative method analyses of trait evolution, with a flexible framework for users ... define their own novel models of trait evolution, involving both ’intrinsic’ and ’extrinsic’ factors (respective ... TreEvo is adapted only for univariate, continuous traits...
  • Phylocom

  • Referenced in 3 articles [sw27224]
  • structure and character evolution. The increasing availability of phylogenetic and trait data for communities ... numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented ... measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow...
  • BayesTraits

  • Referenced in 1 article [sw35903]
  • computer package for performing analyses of trait evolution among groups of species for which ... applied to the analysis of traits that adopt a finite number of discrete states ... continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states ... about correlations among traits. The method can be used to take into account uncertainty about...
  • TASSEL

  • Referenced in 5 articles [sw11446]
  • population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear...
  • POUMM

  • Referenced in 1 article [sw19422]
  • phylogenetic heritability of continuous traits, to test hypotheses of neutral evolution versus stabilizing selection ... error and to make predictions about the evolution of a phenotype and phenotypic variation ... simulation of a univariate continuous trait evolution along a phylogenetic tree. A quick example...
  • surface

  • Referenced in 1 article [sw26124]
  • surface: Fitting Hansen Models to Investigate Convergent Evolution. SURFACE is a data-driven phylogenetic comparative ... fitting stabilizing selection models to continuous trait data, building on the ouch package. The main ... stepwise AIC, then identify cases of convergent evolution where multiple lineages have shifted...
  • ForSim

  • Referenced in 2 articles [sw35346]
  • Many important problems in biology involve complex traits affected by multiple coding or regulatory parts ... simulation tool for exploring the consequences of evolution by phenotype, whereby demographic, chance, behavioral...
  • SIMMAP

  • Referenced in 1 article [sw21252]
  • SIMMAP: Stochastic character mapping of discrete traits on phylogenies. Background: Character mapping on phylogenies ... understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony...
  • METRADE

  • Referenced in 1 article [sw28181]
  • multi-omic network models. Bacterial phenotypic traits and lifestyles in response to diverse environmental conditions ... short term multi-omic (transcriptomic and metabolic) evolution, thus enabling comparative analysis of metabolic conditions...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12074 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • Graphviz

  • Referenced in 81 articles [sw01283]
  • Graphviz is open source graph visualization software. Graph...
  • Smalltalk

  • Referenced in 189 articles [sw01561]
  • Smalltalk is an object-oriented, dynamically typed, reflective...
  • ANTLR

  • Referenced in 57 articles [sw03062]
  • ANTLR (ANother Tool for Language Recognition) is a...