• MOEA/D

  • Referenced in 277 articles [sw06583]
  • MOEA/D framework. An experimental analysis of evolutionary heuristics for the biobjective traveling purchaser problem (2TPP...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. The Molecular ... Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous ... species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein ... addition to the tools for statistical analysis of data, MEGA provides many convenient facilities...
  • 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 ... formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data ... expanded well beyond its central role in evolutionary biology, now encompassing applications in areas...
  • KEEL

  • Referenced in 156 articles [sw06791]
  • evolutionary learning techniques with different pre-processing techniques, allowing it to perform a complete analysis...
  • PSPManalysis

  • Referenced in 18 articles [sw20475]
  • procedures for the demographic, bifurcation and evolutionary analysis of physiologically structured population models (PSPMs), which...
  • Mesquite

  • Referenced in 16 articles [sw09680]
  • Mesquite: A modular system for evolutionary analysis. Mesquite is modular, extendible software for evolutionary biology ... about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population...
  • BEAUti

  • Referenced in 17 articles [sw12589]
  • Bayesian Evolutionary Analysis Utility (BEAUti). BEAUti is a graphical user-interface (GUI) application for generating...
  • Rapide

  • Referenced in 38 articles [sw01249]
  • EADLs in evolutionary development and rigorous analysis of large-scale systems. Rapide™ is designed...
  • GEIGER

  • Referenced in 12 articles [sw18726]
  • package geiger: Analysis of Evolutionary Diversification. Methods for fitting macroevolutionary models to phylogenetic trees...
  • PhyloNet

  • Referenced in 11 articles [sw20725]
  • evolutionary network reconstruction: reconstructing an evolutionary network from a species tree ... allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly...
  • SplitsTree

  • Referenced in 32 articles [sw12234]
  • interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports ... transformations, the computation of parsimony splits, spectral analysis and bootstrapping...
  • MEGA6

  • Referenced in 3 articles [sw16250]
  • MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. We announce the release of an advanced version ... Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments ... inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables ... search for the optimal trees under evolutionary criteria and implements a more advanced memory management...
  • rVISTA

  • Referenced in 4 articles [sw18501]
  • rVISTA 2.0: evolutionary analysis of transcription factor binding sites. dentifying and characterizing the transcription factor ... often conserved between related species. Using this evolutionary principle, we have created a comparative tool ... fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs...
  • emoa

  • Referenced in 5 articles [sw14382]
  • building blocks for the design and analysis of evolutionary multiobjective optimization algorithms...
  • BEAST

  • Referenced in 60 articles [sw12588]
  • cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured ... also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST...
  • adephylo

  • Referenced in 3 articles [sw08303]
  • software dedicated to the analysis of comparative evolutionary data. Phylogenetic comparative methods initially aimed ... effects of phylogenetic signal in the analysis of biological traits. However, recent approaches have shown ... examination of phylogenetic structures can unveil interesting evolutionary patterns. For this purpose, we developed ... open up new perspectives in the analysis of evolutionary comparative data...
  • PAML

  • Referenced in 43 articles [sw10916]
  • Phylogenetic Analysis by Maximum Likelihood (PAML). PAML is a package of programs for phylogenetic analyses ... parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using...
  • pegas

  • Referenced in 4 articles [sw08307]
  • pegas: Population and Evolutionary Genetics Analysis System. pegas provides functions for reading, writing, plotting, analysing...
  • rWind

  • Referenced in 2 articles [sw31313]
  • Currents Data in Ecological and Evolutionary Analysis. Tools for download and manage surface wind...
  • 2D-MH

  • Referenced in 21 articles [sw19727]
  • useful insights for performing large-scale analysis. Here, a new two-dimensional graph, called ... used as a metric for the “evolutionary distance” of a protein from one species ... become a useful vehicle for large-scale analysis of the avalanche of protein sequences generated ... number of protein sequences and compare the evolutionary distances between them...