• fastDNAml

  • Referenced in 91 articles [sw06651]
  • program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. Much of this program ... information on fastDNAml). For Felsenstein’s phylogenetic analysis software, including the latest versions of DNAML...
  • PAUP*

  • Referenced in 49 articles [sw07834]
  • PAUP*: phylogenetic analysis under parsimony. PAUP* version 4.0 is a major upgrade and new release ... molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central ... success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most ... guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well...
  • ape

  • Referenced in 47 articles [sw04569]
  • package ape: Analyses of Phylogenetics and Evolution , ape provides functions for reading, writing, plotting ... manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses ... tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute...
  • PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • perl package and an alignment tool for phylogenetic networks. Phylogenetic networks are a generalization ... phylogenetic trees that allow for the representation of evolutionary events acting at the population level ... lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms ... phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none...
  • PAML

  • Referenced in 34 articles [sw10916]
  • Phylogenetic Analysis by Maximum Likelihood (PAML). PAML is a package of programs for phylogenetic analyses...
  • MrBayes

  • Referenced in 43 articles [sw07715]
  • model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain...
  • BEAST

  • Referenced in 41 articles [sw12588]
  • cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured...
  • T-coffee

  • Referenced in 39 articles [sw13195]
  • cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests...
  • Seq-Gen

  • Referenced in 30 articles [sw08310]
  • Carlo simulation of molecular sequence evolution along phylogenetic trees. Seq-Gen is a program that...
  • phytools

  • Referenced in 13 articles [sw10003]
  • package phytools: Phylogenetic Tools for comparative biology (and other things): Package contains various functions ... phylogenetic analysis. This functionality is concentrated in the phylogenetic analysis of comparative data from species ... multiple (i.e., partial) Mantel test; fitting a phylogenetic regression model with error in predictor ... response variables; conducting a phylogenetic principal components analysis, a phylogenetic regression, a reduced major axis...
  • metafor

  • Referenced in 27 articles [sw12291]
  • known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted...
  • MEGA

  • Referenced in 25 articles [sw09078]
  • results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here...
  • Dendroscope

  • Referenced in 12 articles [sw21230]
  • Dendroscope: An interactive viewer for large phylogenetic trees. BACKGROUND: Research in evolution requires software ... visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression ... interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations ... user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets...
  • Mesquite

  • Referenced in 14 articles [sw09680]
  • 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...
  • PANTHER

  • Referenced in 14 articles [sw22973]
  • other gene attributes, in the context of phylogenetic trees. The data and tools in PANTHER ... protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse...
  • RAxML

  • Referenced in 12 articles [sw07716]
  • phylogeny with maximum likelihood. Inference of large phylogenetic trees with statistical methods is computationally intensive ... RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains...
  • CLUSTAL

  • Referenced in 17 articles [sw12750]
  • method is based on first deriving a phylogenetic tree from a matrix of all pairwise...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output...
  • Footprinter

  • Referenced in 10 articles [sw09003]
  • FootPrinter: a program designed for phylogenetic footprinting. Phylogenetic footprinting is a method for the discovery ... this purpose, making use of the phylogenetic relationships among the homologous sequences in order...
  • GRAPPA

  • Referenced in 11 articles [sw17255]
  • Linear programming for phylogenetic reconstruction based on gene rearrangements. Phylogenetic reconstruction from gene rearrangements...