• Scatter Search

  • Referenced in 283 articles [sw05291]
  • neural networks. Scatter search is an evolutionary method that has been successfully applied ... context knowledge. In contrast to other evolutionary methods like genetic algorithms, scatter search is founded...
  • SPEA2

  • Referenced in 436 articles [sw06686]
  • Algorithm 2: SPEA2 in an elitist multiobjective evolutionary algorithm. It is an improved version ... estimation technique, and an enhanced archive truncation method. SPEA2 operates with a population (archive...
  • MSOPS-II

  • Referenced in 12 articles [sw11982]
  • general-purpose many-objective optimiser. Existing evolutionary methods capable of true many-objective optimisation have...
  • MrBayes

  • Referenced in 47 articles [sw07715]
  • phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate...
  • CMA-ES

  • Referenced in 100 articles [sw05063]
  • Evolution strategies (ES) are stochastic, derivative-free methods for numerical optimization of non-linear ... problems. They belong to the class of evolutionary algorithms and evolutionary computation. An evolutionary algorithm ... covariance matrix adaptation (CMA) is a method to update the covariance matrix of this distribution...
  • GEIGER

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

  • Referenced in 10 articles [sw14304]
  • evtree: Evolutionary Learning of Globally Optimal Trees. Commonly used classification and regression tree methods like ... trees is to use global optimization methods like evolutionary algorithms. The evtree package implements...
  • BEAST

  • Referenced in 44 articles [sw12588]
  • method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning...
  • GEATbx

  • Referenced in 20 articles [sw08590]
  • Algorithm Toolbox for Matlab. The Genetic and Evolutionary Algorithm Toolbox provides global optimization capabilities ... GEATbx should be your method of choice! Powerful genetic and evolutionary algorithms find solutions...
  • PhyloNet

  • Referenced in 9 articles [sw20725]
  • studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design ... analyze large data set using new computational methods...
  • D2MOPSO

  • Referenced in 4 articles [sw09958]
  • state-of-the-art decomposition based evolutionary methods...
  • SHARK

  • Referenced in 15 articles [sw13542]
  • systems. It comprises methods for single- and multi-objective optimization (e.g., evolutionary and gradient-based...
  • MEGA4

  • Referenced in 7 articles [sw07695]
  • evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility ... natural language descriptions of the models and methods used in the analyses. This facility aims ... Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously ... substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion...
  • rgenoud

  • Referenced in 26 articles [sw08657]
  • that combines evolutionary search algorithms with derivative-based (Newton or quasi-Newton) methods to solve...
  • ape

  • Referenced in 55 articles [sw04569]
  • data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean ... BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices...
  • Proofwatch

  • Referenced in 3 articles [sw28654]
  • dynamically updated notion of proof matching. The methods are evaluated on a large ... strategies invented for Mizar by evolutionary methods...
  • EFICAz

  • Referenced in 3 articles [sw35281]
  • inference that combines predictions from four different methods developed and optimized to achieve high prediction ... family) identification, we have developed an Evolutionary Footprinting method that uses evolutionary information from homofunctional...
  • GRAPPA

  • Referenced in 11 articles [sw17255]
  • expensive scoring procedure. We have implemented this method within our GRAPPA software and run several ... very large evolutionary distances, consistently beating the baseline Neighbor-Joining. Our new method enables ... range of applicability of the direct optimization method to chromosomes of size comparable to those ... datasets with complex combinations of evolutionary events...
  • CIXL2

  • Referenced in 19 articles [sw03302]
  • features. We propose a crossover operator for evolutionary algorithms with real values that is based ... obtained are above the performance of standard methods...