• PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • only a few applications to work with phylogenetic networks, none of which are open-source ... allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning...
  • phytools

  • Referenced in 13 articles [sw10003]
  • comparative biology (and other things): Package contains various functions for phylogenetic analysis. This ... functionality is concentrated in the phylogenetic analysis of comparative data from species. For example ... regression, a phylogenetic canonical correlation analysis, and a phylogenetic ANOVA; projecting a tree onto ... threshold model. In addition to this phylogenetic comparative method functionality, the package also contains functions...
  • Mesquite

  • Referenced in 14 articles [sw09680]
  • Mesquite: A modular system for evolutionary analysis. Mesquite is modular, extendible software for evolutionary biology ... analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some...
  • adephylo

  • Referenced in 3 articles [sw08303]
  • adephylo: new tools for investigating the phylogenetic signal in biological traits. adephylo is a package ... software dedicated to the analysis of comparative evolutionary data. Phylogenetic comparative methods initially aimed ... effects of phylogenetic signal in the analysis of biological traits. However, recent approaches have shown ... phylogenetic structures. These tools open up new perspectives in the analysis of evolutionary comparative data...
  • PAUP*

  • Referenced in 51 articles [sw07834]
  • serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well ... even more indispensable tool in comparative biological analysis than were previous editions of the program...
  • RAxML

  • Referenced in 34 articles [sw07716]
  • cases yields super-linear speedups for an analysis of 1.000 organisms on a LINUX cluster ... RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains ... Eukarya, Bacteria and Archaea. Finally, we compare the sequential speed and accuracy of RAxML...
  • PhyloNetworks

  • Referenced in 1 article [sw29667]
  • multi-locus sequences (SNaQ), with possible bootstrap analysis. PhyloNetworks is the first software providing tools ... support. Networks can be used for phylogenetic comparative analysis of continuous traits, to estimate ancestral...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • desktop application designed for comparative analysis of homologous gene sequences either from multigene families ... addition to the tools for statistical analysis of data, MEGA provides many convenient facilities ... results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here...
  • Tanglegrams

  • Referenced in 4 articles [sw21231]
  • task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies ... tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines ... increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly ... formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach...
  • CLUSS

  • Referenced in 2 articles [sw22946]
  • terms of phylogenetic analysis and prediction of biological functions. Compared to existing clustering methods, CLUSS...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step ... sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN ... assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output...
  • CoMeta

  • Referenced in 2 articles [sw25789]
  • Comparing metabolic pathways through reactions and potential fluxes. Comparison ... metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases ... literature many techniques have been proposed to compare metabolic pathways. Most of them focus...
  • Phylo-MCOA

  • Referenced in 2 articles [sw18727]
  • individual gene and species produce the same phylogenetic tree and are thus likely to share ... inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced...
  • RepeatExplorer

  • Referenced in 1 article [sw23829]
  • resources that would enable large-scale repeat analysis to be run by biologically oriented researchers ... identified repeats, investigate phylogenetic relationships of retroelements and perform comparative analysis of repeat composition between...
  • TaxMan

  • Referenced in 1 article [sw35407]
  • Trees resulting from phylogenetic analysis can also be stored, and compared with a reference taxonomy...
  • RAST

  • Referenced in 7 articles [sw17158]
  • public resource for the automatic phylogenetic and functional analysis of metagenomes. Background: Random community genomes ... metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes ... paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data...
  • TOPD/FMTS

  • Referenced in 5 articles [sw19992]
  • Partition method, Triplets or Quartets) to compare phylogenetic trees. One of the novelties of this ... option is also complemented with a randomization analysis to test the null hypothesis that...
  • CDAOstore

  • Referenced in 4 articles [sw06415]
  • field of evolutionary biology and phylogenetic analysis. The novelty of CDAOStore lies ... derived from studies of querying requirements for phylogenetic databases.par CDAOStore represents the first full implementation ... composed of a formal ontology (the comparative data analysis ontology), an XML exchange format (NeXML...
  • OrthoMCL

  • Referenced in 14 articles [sw29602]
  • genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences ... Methods successfully exploited for prokaryotic genome analysis have proved difficult to apply to eukaryotes, however ... based on individual genes or user-defined phylogenetic patterns (http://www.cbil.upenn.edu/gene-family). Analysis of clusters...
  • tracker2

  • Referenced in 1 article [sw15710]
  • phylogenetic footprinting, a technique used to identify regulatory elements by comparative sequence analysis. Based...