Software

From MolEvol

Alignment

Phylogenetic tree building and analysis

Post-Hoc Tree Analysis or manipulation

  • DendroPy (Fantastic for summarizing posteriors, distance calculations, and simulation)
  • Newick Utilities (Rerooting and tree parsing from the command line)

Tree Viewing and Plotting

  • FigTree
  • ggTree (R package for producing publication-quality trees with metadata)

Other

Pipelines

  • Agalma (Transcriptome assembly and analysis)
  • ipyrad (RADseq data assembly and analysis)

Population analysis

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