• PAUP*

  • Referenced in 57 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...
  • RAxML

  • Referenced in 44 articles [sw07716]
  • taxon phylogeny with maximum likelihood. Inference of large phylogenetic trees with statistical methods is computationally ... addition, we use RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from...
  • MrBayes

  • Referenced in 60 articles [sw07715]
  • Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes...
  • T-REX

  • Referenced in 9 articles [sw20724]
  • server for inferring, validating and visualizing phylogenetic trees and networks. T-REX (Tree and reticulogram ... reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer ... Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence ... comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices...
  • INDELible

  • Referenced in 8 articles [sw23043]
  • testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited ... including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction...
  • BEAGLE

  • Referenced in 6 articles [sw12586]
  • Performance Computing Library for Statistical Phylogenetics. Phylogenetic inference is fundamental to our understanding of most ... interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large ... point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would ... library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing...
  • MEGA4

  • Referenced in 7 articles [sw07695]
  • sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version...
  • AWTY

  • Referenced in 4 articles [sw18698]
  • exploration of MCMC convergence in Bayesian phylogenetic inference. AWTY is a system for graphical exploration ... Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. The graphics produced by AWTY are designed...
  • Statalign

  • Referenced in 5 articles [sw16609]
  • most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple ... substitutions as phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions...
  • GASTS

  • Referenced in 5 articles [sw29624]
  • GASTS, an algorithm for scoring a fixed phylogenetic tree: given a tree and a collection ... ordered list of syntenic blocks, GASTS infers genomes for the internal nodes of the tree ... ancestral reconstruction of large genomes and phylogenetic inference for high-resolution vertebrate genomes...
  • MURPAR

  • Referenced in 2 articles [sw29666]
  • MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. Phylogenetic networks ... gene transfer (HGT). One approach for inferring phylogenetic networks is based on reconciling gene trees ... address the computational problem of inferring phylogenetic networks with minimum reticulations from a collection ... present an efficient heuristic, MURPAR, for inferring a phylogenetic network from a collection of gene...
  • ALFRED

  • Referenced in 2 articles [sw22013]
  • many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale ... text]. By applying our program to phylogenetic inference as a case study, we find that ... exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate...
  • CodonPhyML

  • Referenced in 2 articles [sw23036]
  • models. Thus, for protein-coding genes, phylogenetic inference is expected to be more accurate under ... fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models ... largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated ... includes most recent fast methods for estimating phylogenetic branch supports and provides an integral framework...
  • MEGA6

  • Referenced in 3 articles [sw16250]
  • contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis...
  • BMGE

  • Referenced in 3 articles [sw23046]
  • sequence alignment that are suited for phylogenetic inference. BMGE selects characters that are biologically relevant...
  • PhyloNetworks

  • Referenced in 3 articles [sw29667]
  • package for phylogenetic networks. PhyloNetworks is a Julia package for the inference, manipulation, visualization ... phylogenetic networks in an interactive environment. Inference of phylogenetic networks is done with maximum pseudolikelihood...
  • PBPI

  • Referenced in 1 article [sw09015]
  • high performance implementation of Bayesian phylogenetic inference. This paper describes the implementation and performance ... PBPI, a parallel implementation of Bayesian phylogenetic inference method for DNA sequence data. By combining ... likelihood-based assessment of phylogenies, Bayesian phylogenetic inferences can incorporate complex statistic models into ... significant performance improvement over comparable Bayesian phylogenetic inference programs. We evaluated the performance and accuracy...
  • PANTHER

  • Referenced in 15 articles [sw22973]
  • other gene attributes, in the context of phylogenetic trees. The data and tools in PANTHER ... inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic ... designed to represent gene family evolution, including inference of evolutionary events, such as speciation...
  • SATe

  • Referenced in 3 articles [sw24610]
  • software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated ... aligned and further merged for phylogenetic tree inference. The implementation developed at the University...
  • FastTree

  • Referenced in 9 articles [sw28979]
  • Distance Matrix. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein...