• RAxML

  • Referenced in 41 articles [sw07716]
  • taxon phylogeny with maximum likelihood. Inference of large phylogenetic trees with statistical methods is computationally ... 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...
  • 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 ... used software package for the inference of evolutionary trees. In addition, the PAUP manual...
  • T-REX

  • Referenced in 8 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 ... 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 7 articles [sw23043]
  • including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction...
  • MEGA4

  • Referenced in 7 articles [sw07695]
  • sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version...
  • 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...
  • 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 ... histories. The trees are now designed to represent gene family evolution, including inference of evolutionary...
  • FastTree

  • Referenced in 7 articles [sw28979]
  • Distance Matrix. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein...
  • MergeAlign

  • Referenced in 2 articles [sw24604]
  • single matrix of amino acid substitution. Phylogenetic trees inferred from these MergeAlign alignments have better ... select accurately aligned data for downstream phylogenetic applications...
  • CloudPhylo

  • Referenced in 2 articles [sw22014]
  • high efficiency and good scalability on phylogenetic tree inference. Availability and Implementation:https://github.com/XingjianXu/cloudphylo...
  • Phylo-MCOA

  • Referenced in 2 articles [sw18727]
  • explored on a regular basis to infer phylogenetic trees, but there are often discordances among...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • Entrez Gene. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified...
  • MURPAR

  • Referenced in 2 articles [sw29666]
  • fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. Phylogenetic networks provide ... approach for inferring phylogenetic networks is based on reconciling gene trees, assuming all incongruence among ... inferring phylogenetic networks with minimum reticulations from a collection of gene trees. As this problem ... MURPAR, for inferring a phylogenetic network from a collection of gene trees by using pairwise...
  • PhyNav

  • Referenced in 1 article [sw36933]
  • fewer sequences but contains most relevant phylogenetic information from the whole dataset. For this reduced ... scaffold to construct the full tree. Because many minimal subsets exist the procedure is repeated ... optimality criterion is considered as the inferred phylogenetic tree. PhyNav gives encouraging results compared...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • different species with a special emphasis on inferring evolutionary relationships and patterns ... obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss...
  • TreeClone

  • Referenced in 1 article [sw30711]
  • phylogenetic tree prior. The use of the tree structure in the prior greatly strengthens inference ... subclones that can be explained by a phylogenetic tree are assigned non-negligible probabilities ... cellular proportions and the phylogenetic tree spanned by the inferred subclones. The proposed method...
  • pIQPNNI

  • Referenced in 3 articles [sw12591]
  • IQPNNI is a program to infer maximum-likelihood phylogenetic trees from DNA or protein data...
  • Secator

  • Referenced in 2 articles [sw12606]
  • Secator : a program for inferring protein subfamilies from phylogenetic trees. With the huge increase...
  • iGTP

  • Referenced in 4 articles [sw23050]
  • software package for large-scale gene tree parsimony analysis. BACKGROUND: The ever-increasing wealth ... scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees...
  • ADAPTSITE

  • Referenced in 1 article [sw35900]
  • coding sequences for a given phylogenetic tree. The program infers ancestral codons at all interior...