Software

• Heterogeneity test: Coalescent test for differences in allele frequency distributions
• [Download] [Instructions] [Citation]
• CAFE: Computational analysis of (gene) family evolution
• CAFE v5: [Website] [Citation]
• Dfoil: Introgression testing for a five-taxon phylogeny
• [Download] [Citation]
• AGOUTI: Improving assembly and annotation using RNA-seq
• [Download] [Example assembly and annotation] [Citation]
• GRAMPA: Gene-tree reconciliation algorithm using MUL-trees for polyploid analysis
• [Download] [Citation]
• PePo: Probabilities of hemiplasy versus probabilities of homoplasy
• [Download] [Citation]
• Referee: Genome assembly quality scores
• [Download] [Citation]
• HeIST: Hemiplasy Inference Tool (for discrete traits)
• [Download] [Citation]
• sCF: Site concordance factors
• [Download] [Citation (parsimony version)] [Citation (likelihood version)]
• CAGEE: Computational Analysis of Gene Expression Evolution
• [Website] [Citation]
• seastaR: Construct a phylogenetic covariance matrix with discordance
• [Download] [Citation]
• phyloGAN: Phylogenetic generative adversarial network
• [Download] [Citation]
• NoDEAR: No Disequilibrium Estimation of Accurate Recombination
• [Download] [Citation]
• reconcILS: Gene tree-species tree reconciliation with ILS
• [Download] [Citation]
• dupcoal: Coalescent simulator with duplication and loss under the MSC-DL model
• [Download] [Citation]

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