• PAUP*

  • Referenced in 57 articles [sw07834]
  • well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse ... conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis ... used software package for the inference of evolutionary trees. In addition, the PAUP manual ... even more indispensable tool in comparative biological analysis than were previous editions of the program...
  • CMA-ES

  • Referenced in 121 articles [sw05063]
  • computation. An evolutionary algorithm is broadly based on the principle of biological evolution, namely...
  • Mesquite

  • Referenced in 16 articles [sw09680]
  • Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze...
  • GASTS

  • Referenced in 5 articles [sw29624]
  • study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models...
  • CDAOstore

  • Referenced in 4 articles [sw06415]
  • studies in the field of evolutionary biology and phylogenetic analysis. The novelty of CDAOStore lies...
  • ALF

  • Referenced in 2 articles [sw37905]
  • Framework for Genome Evolution. In computational evolutionary biology, verification and benchmarking is a challenging task ... because the evolutionary history of studied biological entities is usually not known. Computer programs ... aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon...
  • SEGM

  • Referenced in 5 articles [sw30070]
  • sense (past–present) and in the inverse evolutionary sense (present–past). The genetic motifs studied ... date the only computational biology software in this evolutionary approach...
  • laird-jtb2018

  • Referenced in 1 article [sw39195]
  • Cooperation is a central topic in evolutionary biology because (a) it is difficult to reconcile ... successively higher levels of biological organization. Within evolutionary game theory, the Prisoner’s Dilemma...
  • PhyloNet

  • Referenced in 10 articles [sw20725]
  • reticulate evolutionary relationships. BACKGROUND: Phylogenies, i.e., the evolutionary histories of groups of taxa, play ... major role in representing the interrelationships among biological entities. Many software tools for reconstructing ... almost all of which assume the underlying evolutionary history to be a tree. While trees...
  • OMICtools

  • Referenced in 1 article [sw29600]
  • grand challenges in evolutionary biology. As the number of trees grows superexponentially with the number ... species for which an evolutionary tree is reconstructed, tree inference is considered a hard problem...
  • TriLoNet

  • Referenced in 1 article [sw36903]
  • distance between level-1 networks. In evolutionary biology, phylogenetic networks are constructed to represent ... that is slightly more general than an evolutionary tree), here we propose a cubic-time...
  • SAS/Genetics

  • Referenced in 1 article [sw25735]
  • central to medicine, agriculture, evolutionary biology, and forensic science. The inherent variation in genetic data...
  • TreeSwift

  • Referenced in 1 article [sw32580]
  • package. Phylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt...
  • LexStat

  • Referenced in 1 article [sw42153]
  • sequence comparison in historical linguistics and evolutionary biology into a new framework which closely models...
  • adephylo

  • Referenced in 3 articles [sw08303]
  • tools for investigating the phylogenetic signal in biological traits. adephylo is a package ... software dedicated to the analysis of comparative evolutionary data. Phylogenetic comparative methods initially aimed ... phylogenetic signal in the analysis of biological traits. However, recent approaches have shown that considerable ... examination of phylogenetic structures can unveil interesting evolutionary patterns. For this purpose, we developed...
  • GEDEVO

  • Referenced in 3 articles [sw08298]
  • GEDEVO: an evolutionary graph edit distance algorithm for biological network alignment. With the so-called ... graph comparison dedicated to real-world size biological networks. Underlying our approach ... insertions and deletions. We present a novel evolutionary algorithm aiming to minimize ... constantly exploding number and size of available biological networks. The software as well...
  • inspyred

  • Referenced in 5 articles [sw29034]
  • framework for creating biologically-inspired computational intelligence algorithms in Python, including evolutionary computation, swarm intelligence...
  • FRESCO

  • Referenced in 1 article [sw22990]
  • Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available...
  • Plant-mPLoc

  • Referenced in 27 articles [sw22435]
  • Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present ... ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo...
  • Phylotastic

  • Referenced in 0 articles [sw27487]
  • manipulating, and evolving phylogenetic biology workflows using logic programming. Evolutionary Biologists have long struggled with ... reuse of phylogenetic knowledge. An evolutionary biology workflow can be viewed as a plan which ... years ago as a collaboration between evolutionary biologists and computer scientists, with the goal...