• phylodyn

  • Referenced in 3 articles [sw19813]
  • package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric...
  • REJECTOR

  • Referenced in 3 articles [sw24737]
  • Through coalescent simulation, REJECTOR generates numerous gene genealogies, and hence simulated data, under a model...
  • Rsampletrees

  • Referenced in 0 articles [sw19680]
  • package Rsampletrees. MCMC Sampling of Gene Genealogies Conditional on Genetic Data. Sample ancestral trees conditional...
  • TreeDT

  • Referenced in 2 articles [sw37015]
  • predicts likely locations of a disease susceptibility gene. TreeDT extracts, essentially in the form ... chromosomal location is an estimate of the genealogy of the haplotypes. TreeDT constructs these trees ... history for those and a likely disease gene location? We give a detailed description...
  • gatars

  • Referenced in 1 article [sw30171]
  • locus association testing in subjects with arbitrary genealogical relationships. Genome-wide sequencing enables evaluation ... between traits and combinations of variants in genes and pathways. But such evaluation requires multi...
  • PedGenie

  • Referenced in 4 articles [sw35514]
  • genetic association testing in extended pedigrees and genealogies of arbitrary size. Background: We present ... nucleotide polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast...
  • Hybrid-Lambda

  • Referenced in 1 article [sw34310]
  • software package that can simulate gene trees within a rooted species network or a rooted ... standard Kingman coalescent process, which produces bifurcating genealogies, or two other Lambda coalescent processes, which...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • CRAN

  • Referenced in 552 articles [sw04351]
  • R is ‘GNU S’, a freely available language...
  • ggplot2

  • Referenced in 365 articles [sw04557]
  • R package ggplot2: An implementation of the Grammar...
  • igraph

  • Referenced in 209 articles [sw07066]
  • igraph is a software package for complex network...
  • Cytoscape

  • Referenced in 80 articles [sw09080]
  • Cytoscape: A Software Environment for Integrated Models of...
  • Arlequin

  • Referenced in 5 articles [sw11442]
  • Arlequin (version 3.0): An integrated software package for...
  • LAMARC

  • Referenced in 7 articles [sw11443]
  • Lamarc 2.0: maximum likelihood and Bayesian estimation of...
  • simuPOP

  • Referenced in 6 articles [sw11732]
  • simuPOP: a forward-time population genetics simulation environment...
  • BEAST

  • Referenced in 59 articles [sw12588]
  • BEAST 2 is a cross-platform program for...
  • BEAUti

  • Referenced in 17 articles [sw12589]
  • Bayesian Evolutionary Analysis Utility (BEAUti). BEAUti is a...
  • shiny

  • Referenced in 112 articles [sw13816]
  • R package shiny: Web Application Framework for R...
  • BUCKy

  • Referenced in 7 articles [sw23619]
  • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance...