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  • PHYLIP
  • Referenced in 103 articles [sw07694]
  • free package of programs for inferring phylogenies. It is distributed as source code, documentation files...

  • BEAST

  • Referenced in 60 articles [sw12588]
  • molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models ... used as a method of reconstructing phylogenies but is also a framework for testing evolutionary...

  • ape
  • Referenced in 63 articles [sw04569]
  • using mean path lengths and penalized likelihood. Phylogeny estimation can be done with...

  • RAxML
  • Referenced in 45 articles [sw07716]
  • Parallel inference of a 10.000-taxon phylogeny with maximum likelihood. Inference of large phylogenetic trees ... that RAxML outperforms the currently fastest statistical phylogeny programs (MrBayes, PHYML) in terms of speed...

  • MrBayes
  • Referenced in 62 articles [sw07715]
  • MrBayes: Bayesian Inference of Phylogeny. MrBayes is a program for Bayesian inference and model choice...

  • Seq-Gen
  • Referenced in 32 articles [sw08310]
  • nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process...

  • SplitsTree
  • Referenced in 32 articles [sw12234]
  • indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing...

  • phytools
  • Referenced in 14 articles [sw10003]
  • taxa; reducing a phylogeny to its backbone tree; dropping tips or adding tips to special ... character state per edge; estimating a phylogeny using the least squares method; simulating birth-death...

  • Bali-phy
  • Referenced in 11 articles [sw16614]
  • simultaneous bayesian inference of alignment and phylogeny. Summary: BAli-Phy is a Bayesian posterior sampler ... explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates ... information in shared insertion/deletions to help infer phylogenies. Availability: Software is available for download...

  • PhyloNet
  • Referenced in 11 articles [sw20725]
  • analyzing and reconstructing reticulate evolutionary relationships. BACKGROUND: Phylogenies, i.e., the evolutionary histories of groups ... software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which...

  • INDELible
  • Referenced in 8 articles [sw23043]
  • sequence evolution. Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies...

  • PhyML
  • Referenced in 11 articles [sw10915]
  • software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences...

  • ASTRAL-II
  • Referenced in 11 articles [sw20492]
  • genes. Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have...

  • CVTree3
  • Referenced in 6 articles [sw22015]
  • Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. A faithful phylogeny...

  • MultiLoc2
  • Referenced in 8 articles [sw22456]
  • MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BACKGROUND: Knowledge...

  • Statalign
  • Referenced in 5 articles [sw16609]
  • phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions ... samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying...

  • HyPhy
  • Referenced in 5 articles [sw23146]
  • HyPhy: hypothesis testing using phylogenies. HyPhy (Hypothesis Testing using Phylogenies) is an open-source software...

  • FastMe
  • Referenced in 5 articles [sw28027]
  • comprehensive, accurate, and fast distance-based phylogeny inference program. FastME provides distance algorithms to infer ... phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor...

  • BitPhylogeny
  • Referenced in 5 articles [sw29661]
  • probabilistic framework for reconstructing intra-tumor phylogenies. Cancer has long been understood as a somatic ... studies, we demonstrate how BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer...

  • RIATA-HGT
  • Referenced in 7 articles [sw17371]
  • factor for any attempt to reconstruct bacterial phylogenies. As a result, detecting and reconstructing...