• PANTHER

  • Referenced in 15 articles [sw22973]
  • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes ... trees are now designed to represent gene family evolution, including inference of evolutionary events, such ... loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers...
  • ProbCons

  • Referenced in 16 articles [sw12014]
  • based multiple sequence alignment. To study gene evolution across a wide range of organisms, biologists...
  • iLoc-Virus

  • Referenced in 31 articles [sw22417]
  • hybridizing the gene ontology information with the sequential evolution information, a predictor called iLoc-Virus...
  • TreeFix

  • Referenced in 6 articles [sw29607]
  • important implications for future investigations of gene evolution. The source code and a sample data...
  • ecceTERA

  • Referenced in 6 articles [sw24891]
  • species tree reconciliation explains the evolution of a gene tree within ... species tree given a model of gene-family evolution. We describe ecceTERA, a program that ... generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well...
  • iLoc-Gpos

  • Referenced in 18 articles [sw22418]
  • hybridizing the information of gene ontology and the sequential evolution information, a novel predictor, called...
  • CAFE

  • Referenced in 3 articles [sw12375]
  • computational tool for the study of gene family evolution. Summary: We present CAFE (Computational Analysis ... gene Family Evolution), a tool for the statistical analysis of the evolution of the size ... death process to model the evolution of gene family sizes over a phylogeny...
  • Notung

  • Referenced in 13 articles [sw08917]
  • Tree. Large scale gene duplication is a major force driving the evolution of genetic functional ... have played an important role in the evolution of the maize, yeast, and vertebrate genomes ... evolutionary trees to analyze the history of gene duplication and estimate duplication times provides ... this process. Many studies in the molecular evolution literature have used this approach on small...
  • Gneg-mPLoc

  • Referenced in 16 articles [sw25879]
  • incorporating the information of gene ontology, functional domain, and sequential evolution, a new predictor called...
  • KELLER

  • Referenced in 4 articles [sw22600]
  • estimating time-varying interactions between genes. MOTIVATION: Gene regulatory networks underlying temporal processes, such ... develop methods that capture the temporal evolution of the regulatory networks. These methods will ... studying the driving forces underlying the dynamic gene regulation circuitry and predicting the future network ... first glimpse into the temporal evolution of gene networks in a living organism during...
  • PseAAC-General

  • Referenced in 16 articles [sw22430]
  • gene ontology mode, the functional domain mode, and the sequential evolution mode. This program allows...
  • MEGA

  • Referenced in 35 articles [sw09078]
  • application designed for comparative analysis of homologous gene sequences either from multigene families or from ... relationships and patterns of DNA and protein evolution. In addition to the tools for statistical...
  • LTR_FINDER

  • Referenced in 3 articles [sw13196]
  • They play important roles in the evolution of genes and genomes. Ever-growing amount...
  • SimPhy

  • Referenced in 5 articles [sw17058]
  • model in which the evolution of species, locus, and gene trees is governed by global...
  • RANGER-DTL

  • Referenced in 1 article [sw34144]
  • RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Summary ... software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software ... many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple...
  • Aevol

  • Referenced in 1 article [sw40802]
  • Inspired by bacterial genomics and experimental microbial evolution research, Aevol has a detailed and realistic ... genome characterized by potentially varying number of genes, genetic architecture, and coding/non-coding sequence proportion. Aevol ... organism properties over the course of evolution. An extension of the model (R-Aevol), contains ... allowing for the study of the evolution of gene regulation networks...
  • BiGGEsTS

  • Referenced in 2 articles [sw23417]
  • retrieving potentially relevant information from the gene expression data, relying either on visualization or additional ... data. Visualization includes colored matrices, expression evolution charts and pattern charts, as well as dendograms ... applying hierarchical clustering algorithms on the gene expression data and ontology graphs highlighting the relevant ... extract subsets of genes that exhibit coherent expression evolutions in specific subsets of experimental conditions...
  • CYNTENATOR

  • Referenced in 1 article [sw29670]
  • vertebrate genomes. Whole genome gene order evolution in higher eukaryotes was initially considered...
  • Babelomics

  • Referenced in 6 articles [sw36144]
  • gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which...
  • OrthoMCL

  • Referenced in 15 articles [sw29602]
  • useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically ... larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides...