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Mesquite is a modular software system for evolutionary analysis, designed to help biologists analyze comparative data about organisms. Although its emphasis is on phylogenetic analysis, some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. The analyses include:

  • Reconstruction of ancestral states (parsimony, likelihood)
  • Tests of process of character evolution, including correlation
  • Analysis of speciation and extinction rates
  • Simulation of character evolution (categorical, DNA, continuous)
  • Parametric bootstrapping (integration with programs such as PAUP* and NONA)
  • Morphometrics (PCA, CVA, geometric morphometrics)
  • Coalescence (simulations, other calculations)
  • Tree comparisons and simulations (tree similarity, Markov speciation models)

Mesquite is not primarily designed to infer phylogenetic trees, but rather for diverse analyses using already inferred trees.

Technical Expertise Required: 
Basic programming skills
Additional Information: 

Example use: Tyler, Kevin M.; Wagner, Gerd K.; Wu, Qiong; Huber, Katharina T., Functional Significance May Underlie the Taxonomic Utility of Single Amino Acid Substitutions in Conserved Proteins,2010, Journal of Molecular Evolution (70:4), DOI: 10.1007/s00239-010-9338-y