Mesquite 2.5: Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. . Mesquite is not primarily designed to infer phylogenetic trees, but rather for diverse analyses using already inferred trees.

Cost: $0

Open source: yes

URL: http://mesquiteproject.org/

Reference(s):

Data formats ? :

• NEXUS
• FASTA
• GenBank

Tree formats ? :

• NEXUS

Methods ? and character types ? :

• Fitch ancestral state reconstruction (Wagner/unordered parsimony)
  DNA strict
  RNA strict
  AA strict
  Binary
  Multistate unordered
• Farris ancestral state reconstruction (ordered parsimony)
  Multistate ordered
• Concentrated changes test
  Binary-Binary
• Correlated change in two variables (Pagel Discrete)
  Binary-Binary
• BiSSE
  Binary

Application kind and platform ? :

• Mesquite module: Linux, Mac OS 10.3, Mac OS 10.4, Mac OS 10.5, Unix, Windows 2000, Windows 98, Windows Vista, Windows XP
• standalone application with GUI: Linux, Mac OS 10.3, Mac OS 10.4, Mac OS 10.5, Unix, Windows 2000, Windows 98, Windows Vista, Windows XP