2016
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
Dornburg A, Fisk JN, Tamagnan J, Townsend JP. PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Ecology And Evolution 2016, 16: 262. PMID: 27905871, PMCID: PMC5134231, DOI: 10.1186/s12862-016-0837-3.Peer-Reviewed Original ResearchConceptsParallel processingOpen-source software packageBayesian posterior distributionLack of softwareOpen-source programPhylogenetic experimental designProbability of resolutionUser hardwareData explorationData visualizationNext-generation sequence datasetsInformation contentSource programNovel visualizationPosterior distributionBayesian settingAdditional sample dataPower usersDataset partitionsBayesian approachSequence data setsSoftware packageDatasetGenomic information contentSoftware
2015
Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects
Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Ecology And Evolution 2015, 15: 86. PMID: 25968460, PMCID: PMC4429678, DOI: 10.1186/s12862-015-0364-7.Peer-Reviewed Original ResearchConceptsGeneralized signalCorrect treeAnalytical predictionsNoise analysisDifferent inference methodsBayesian approachLength spaceInference methodsQuartet treesMaximum likelihoodSimulation studyBranch lengthsInferenceModel treePhylogenetic inferenceUtility of charactersAsymmetrical topologyLong-branch effectsConvergenceTopologyPredictionSpaceSignalsEvolution