• Seq-Gen

  • Referenced in 31 articles [sw08310]
  • along a phylogeny, using common models of the substitution process. A range of models...
  • INDELible

  • Referenced in 8 articles [sw23043]
  • indels) as well as substitutions. Indels are simulated under several models of indel-length distribution ... program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary ... nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites ... codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches...
  • Bali-phy

  • Referenced in 11 articles [sw16614]
  • alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information...
  • PhyML

  • Referenced in 11 articles [sw10915]
  • lies in the large number of substitution models coupled to various options to search...
  • BIONJ

  • Referenced in 30 articles [sw08301]
  • taxon model trees to determine BIONJ’s efficiency. When the substitution rates are low (maximum ... only slightly better than NJ. When the substitution rates are higher and vary among lineages ... accuracy. In the latter case, for the model trees and the conditions of evolution tested ... highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions...
  • Statalign

  • Referenced in 5 articles [sw16609]
  • single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies ... save the results. The background model for insertions ... deletions can be combined with any substitution model. It is easy to add new substitution...
  • SimPhy

  • Referenced in 5 articles [sw17058]
  • statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed ... sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy...
  • Partitionfinder

  • Referenced in 3 articles [sw23033]
  • combined selection of partitioning schemes and substitution models for phylogenetic analyses. In phylogenetic analyses ... molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets ... best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes ... users to select partitioning schemes and substitution models using a range of information-theoretic metrics...
  • MODELTEST

  • Referenced in 8 articles [sw08308]
  • MODELTEST: testing the model of DNA substitution. The program MODELTEST uses log likelihood scores...
  • WinALT

  • Referenced in 9 articles [sw01533]
  • based on a formal model called Parallel Substitution Algorithm. The system combines the best features ... representation of massively parallel distributed spatial computations. Model can be described analytically (WinALT simulation language...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • probabilities, similar to Dayhoff’s substitution model of amino acids. This score is designed...
  • DPRml

  • Referenced in 4 articles [sw12590]
  • most extensive sets of DNA substitution models currently available. We are the first...
  • PhyloBayes 3

  • Referenced in 3 articles [sw23037]
  • molecular dating. MOTIVATION: A variety of probabilistic models describing the evolution of DNA or protein ... amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models...
  • ViBe

  • Referenced in 6 articles [sw21740]
  • choosing randomly which values to substitute from the background model. This approach differs from those...
  • CodonPhyML

  • Referenced in 2 articles [sw23036]
  • Maximum Likelihood Phylogeny Estimation under Codon Substitution Models. Markov models of codon substitution naturally incorporate ... sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, phylogenetic inference...
  • xREI

  • Referenced in 2 articles [sw37904]
  • grammars, probabilistic models combining Markov chain substitution models with stochastic grammars, are powerful models...
  • XRate

  • Referenced in 2 articles [sw35404]
  • working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate ... have used xrate to measure codon substitution rates and predict protein and RNA secondary structures...
  • Global Arrays

  • Referenced in 10 articles [sw07425]
  • Unlike other shared-memory environments, the GA model exposes to the programmer the non-uniform ... complement rather than substitute for the message-passing programming model. The programmer is free...
  • CodonTest

  • Referenced in 1 article [sw37906]
  • CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. Codon models of evolution have facilitated ... independent rates of substitution offer improved fit over single rate models. However, these approaches have ... Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths ... organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further...
  • AUTO-MUTE

  • Referenced in 9 articles [sw16878]
  • upon single residue substitutions in proteins with known native structures. Trained models classify independent mutant...