Software

• Heterogeneity test: Coalescent test for differences in allele frequency distributions.
• [Download] [Instructions] [Citation]
• Perlymorphism: A suite of population genetics tools for large DNA sequence datasets.
• [Download] [Manual] [Citation]
• CAFE: Computational analysis of (gene) family evolution.
• CAFE v5: [Website] [Citation]
• CAFE v4: [Website]
• RPGC: Recombinant population genome construction.
• [RPGC page] [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]
• TEFLoN: Transposable element frequency and location navigator.
• [Download] [Citation]
• PePo: Probabilities of hemiplasy versus probabilities of homoplasy.
• [Download] [Citation]
• Referee: Genome assembly quality scores.
• [Download] [Citation]

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