• GRAPPA

  • Referenced in 12 articles [sw17255]
  • Linear programming for phylogenetic reconstruction based on gene rearrangements. Phylogenetic reconstruction from gene rearrangements...
  • Noisy

  • Referenced in 5 articles [sw21022]
  • alignments. MOTIVATION: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously ... resulting in sometimes misleading signals in phylogenetic reconstruction. RESULTS: We present here a method that ... appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices ... employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever...
  • T-REX

  • Referenced in 9 articles [sw20724]
  • visualizing phylogenetic trees and networks. T-REX (Tree and reticulogram REConstruction ... server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference ... inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms ... included methods allows for validating and visualizing phylogenetic trees and networks which can be built...
  • Quartets MaxCut

  • Referenced in 7 articles [sw29616]
  • divide and conquer quartets algorithm. Accurate phylogenetic reconstruction methods are currently limited to a maximum...
  • PhyloBayes 3

  • Referenced in 3 articles [sw23037]
  • Bayesian software package for phylogenetic reconstruction and molecular dating. MOTIVATION: A variety of probabilistic models ... protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still ... test their ability to jointly improve phylogenetic and dating accuracy. RESULTS: We propose a software ... used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety...
  • Rec-I-DCM3

  • Referenced in 6 articles [sw29614]
  • DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. Phylogenetic trees are commonly reconstructed ... likelihood (ML). Conventional MP heuristics for producing phylogenetic trees produce good solutions within reasonable time ... comparison to existing approaches. Thus, high-quality reconstructions can be obtained for datasets at least...
  • PhyloBayes MPI

  • Referenced in 2 articles [sw23042]
  • PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Modeling across ... important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been ... cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available...
  • BEAST

  • Referenced in 59 articles [sw12588]
  • cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured ... used as a method of reconstructing phylogenies but is also a framework for testing evolutionary...
  • PAML

  • Referenced in 43 articles [sw10916]
  • PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using ... study the evolutionary process, when you have reconstructed trees using other programs such as PAUP...
  • TreeFix

  • Referenced in 6 articles [sw29607]
  • trees. Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications ... TreeFix, a new phylogenetic program for improving gene tree reconstructions. Given a gene tree (preferably ... computed using a maximum-likelihood phylogenetic program), TreeFix finds a “statistically equivalent” gene tree that ... phylogenies and show that it dramatically improves reconstructions compared with current state...
  • Partitionfinder

  • Referenced in 3 articles [sw23033]
  • affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit ... schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python...
  • Phylen

  • Referenced in 1 article [sw28952]
  • Phylen: automatic phylogenetic reconstruction using the EggNOG database. Phylen is an R package that performs ... automatic phylogenetic reconstruction given a set of Hidden Markov Models (HMMs). Genomes are screened against ... single supergene alignment, and a phylogenetic reconstruction is performed and returned as an object...
  • MI-GRAAL

  • Referenced in 3 articles [sw08318]
  • networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time...
  • PTreeRec

  • Referenced in 1 article [sw09656]
  • PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance. Phylogenetic Tree Reconstruction (PTreeRec ... scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method...
  • INDELible

  • Referenced in 8 articles [sw23043]
  • biological sequence evolution. Many methods exist for reconstructing phylogenies from molecular sequence data ... testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited ... multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction...
  • TCS

  • Referenced in 1 article [sw24605]
  • estimate alignment accuracy and improve phylogenetic tree reconstruction. Multiple sequence alignment ... measure can be used to improve phylogenetic tree reconstruction using both an established simulated data ... estimates of structural accuracy and more accurate phylogenetic trees. The software is available from www.tcoffee.org...
  • Phylogeny.fr

  • Referenced in 1 article [sw29599]
  • homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred ... suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors...
  • SPREAD

  • Referenced in 1 article [sw21020]
  • SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. SUMMARY: SPREAD is a user-friendly, cross-platform...
  • STAG

  • Referenced in 1 article [sw40984]
  • availably of suitable data for phylogenetic reconstruction. Here we propose a novel method for species...
  • DPRml

  • Referenced in 4 articles [sw12590]
  • DPRml: distributed phylogeny reconstruction by maximum likelihood. Motivation: In recent years there has been increased ... interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large ... fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood ... based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations...