• SplitsTree

  • Referenced in 30 articles [sw12234]
  • SplitsTree: A program for analyzing and visualizing evolutionary data. MOTIVATION: Real evolutionary data often contain ... SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach...
  • Push

  • Referenced in 11 articles [sw29476]
  • expression of evolving programs within an evolutionary computation system. This article describes Push and illustrates ... evolutionary computation systems, PushGP and Pushpop, are described in detail. PushGP is a genetic programming ... evolves Push programs but does so while simultaneously evolving its own evolutionary mechanisms...
  • MrBayes

  • Referenced in 57 articles [sw07715]
  • program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary...
  • PAML

  • Referenced in 41 articles [sw10916]
  • Likelihood (PAML). PAML is a package of programs for phylogenetic analyses of DNA or protein ... study the evolutionary process, when you have reconstructed trees using other programs such as PAUP...
  • DARWIN

  • Referenced in 3 articles [sw02144]
  • DARWIN: An evolutionary program for nonlinear modeling of chaotic time series. This paper describes ... evolutionary program, DARWIN, to approximate the mathematical model that generates a given time series. DARWIN ... user-friendly. The program is based on an evolutionary algorithms of the same name suggested...
  • PISA

  • Referenced in 61 articles [sw01397]
  • These two modules are implemented as separate programs which communicate through text files. PISA ... problems (test and benchmark problems), selection modules (evolutionary multi-objective optimizers) and modules for performance...
  • Anthill

  • Referenced in 3 articles [sw30590]
  • ideas such as multi-agent and evolutionary programming borrowed from CAS. An Anthill system consists...
  • PUNCH

  • Referenced in 6 articles [sw02447]
  • PUNCH: An evolutionary algorithm for optimizing bit set selection. Nearly every nucleotide-based computing problem ... sequences to represent bits. However, no general program is yet available to optimize those ... this paper, we present a program that uses an evolutionary algorithm to generate optimum ... also test some properties of the program and discuss future applications...
  • BEAST

  • Referenced in 48 articles [sw12588]
  • BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences ... also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST ... standard analyses and a suit of programs for analysing the results...
  • GRAPPA

  • Referenced in 11 articles [sw17255]
  • GESTALT). Our method generates an integer linear program with a carefully limited number of constraints ... rates below 5% up to very large evolutionary distances, consistently beating the baseline Neighbor-Joining...
  • EDDIE

  • Referenced in 13 articles [sw04191]
  • stands for Evolutionary Dynamic Data Investment Evaluator. It is a genetic programming tool designed...
  • GenThreader

  • Referenced in 10 articles [sw35746]
  • family of programs designed to detect distant evolutionary relationships. The original GenThreader algorithm was published...
  • PAUP*

  • Referenced in 55 articles [sw07834]
  • used software package for the inference of evolutionary trees. In addition, the PAUP manual ... analysis than were previous editions of the program and manual. PAUP* 4.0 and MacClade...
  • Hopscotch

  • Referenced in 43 articles [sw00413]
  • Gordon for the numerical solution of evolutionary problems is reformulated and shown to be equivalent ... computing time, storage requirements and ease of programming. Several fairly general conditions are given which...
  • EC++

  • Referenced in 1 article [sw29837]
  • develop programs that explore evolutionary strategy, evolutionary programming, and genetic algorithm methodologies. Moreover the programmer...
  • TREECON

  • Referenced in 1 article [sw33535]
  • Construction and Drawing of Evolutionary Trees. A package of programs (run by a management program ... construction and drawing of evolutionary trees. The program MATRIX calculates dissimilarity values and can perform ... these methods produce unrooted evolutionary trees, a program ROOT places a root on the tree ... Finally, the program DRAW draws the evolutionary tree, changes its size or topology, and produces...
  • JECO

  • Referenced in 1 article [sw33102]
  • techniques such as genetic algorithm, genetic programming, evolutionary mapping methods, particle swarm optimization, ant colonies...
  • fastsimcoal

  • Referenced in 6 articles [sw35122]
  • simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Motivation: Genetic studies focus on increasingly ... present here a new coalescent-based simulation program fastsimcoal, which is able to quickly simulate ... under complex evolutionary scenarios. Availability and Implementation: fastsimcoal is a C++ program compiled for Windows...
  • EVERA

  • Referenced in 1 article [sw02696]
  • EVERA: an evolutionary programming environment for adaptive speech processing. n this paper, we describe EVERA...
  • JCLEC

  • Referenced in 16 articles [sw08869]
  • Java software system for the development of evolutionary computation applications. This system has been designed ... paradigms with a minimum of programming effort. JCLEC architecture comprises three main modules: the core ... knapsack problem by means of evolutionary algorithms...