• 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...
  • ape

  • Referenced in 57 articles [sw04569]
  • reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework ... test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz...
  • RAxML

  • Referenced in 41 articles [sw07716]
  • with maximum likelihood. Inference of large phylogenetic trees with statistical methods is computationally intensive ... recently introduced simple heuristics which yield accurate trees for synthetic as well as real data ... RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains...
  • PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary ... lineages, and lateral gene transfer. While most phylogenetics tools implement ... wide range of algorithms on phylogenetic trees, there exist only a few applications to work...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss...
  • Seq-Gen

  • Referenced in 30 articles [sw08310]
  • simulation of molecular sequence evolution along phylogenetic trees. Seq-Gen is a program that will...
  • 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 ... friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets...
  • PANTHER

  • Referenced in 15 articles [sw22973]
  • gene attributes, in the context of phylogenetic trees. The data and tools in PANTHER ... comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org-have ... function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental...
  • CLUSTAL

  • Referenced in 18 articles [sw12750]
  • based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity...
  • phytools

  • Referenced in 14 articles [sw10003]
  • analysis. This functionality is concentrated in the phylogenetic analysis of comparative data from species ... canonical correlation analysis, and a phylogenetic ANOVA; projecting a tree onto a geographic map; simulating ... adding tips to special types of phylogenetic trees; exporting a tree as an XML file ... visualizations of trees; and a variety of other manipulations and analyses that phylogenetic biologists...
  • PAUP*

  • Referenced in 56 articles [sw07834]
  • PAUP*: phylogenetic analysis under parsimony. PAUP* version 4.0 is a major upgrade and new release ... software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS ... 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...
  • T-REX

  • Referenced in 8 articles [sw20724]
  • server for inferring, validating and visualizing phylogenetic trees and networks. T-REX (Tree and reticulogram ... server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference ... Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence ... fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices...
  • iTOL

  • Referenced in 9 articles [sw33187]
  • Life (iTOL): An Online Tool for Phylogenetic Tree Display and Annotation. Interactive Tree Of Life ... display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted...
  • GEIGER

  • Referenced in 12 articles [sw18726]
  • Methods for fitting macroevolutionary models to phylogenetic trees...
  • ATV

  • Referenced in 8 articles [sw35899]
  • display and manipulation of annotated phylogenetic trees. A Tree Viewer (ATV) is a Java tool ... display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone...
  • apTreeshape

  • Referenced in 8 articles [sw31620]
  • Phylogenetic Treeshape. Simulation and analysis of phylogenetic tree topologies using statistical indices ... additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access...
  • PhyML

  • Referenced in 11 articles [sw10915]
  • options to search the space of phylogenetic tree topologies, going from very fast and efficient...
  • Rec-I-DCM3

  • Referenced in 6 articles [sw29614]
  • fast algorithmic technique for reconstructing large phylogenetic trees. Phylogenetic trees are commonly reconstructed based ... Conventional MP heuristics for producing phylogenetic trees produce good solutions within reasonable time on small...
  • PoMo

  • Referenced in 7 articles [sw35039]
  • incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes ... possible to incur several biases in species tree estimation. Here, we present a simple maximum ... lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown ... model to perform efficient estimation of species trees. We test the performance of PoMo...
  • MEGA4

  • Referenced in 7 articles [sw07695]
  • alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes ... substitution pattern without knowledge of the phylogenetic tree. This new version is a native...