Mesquite (software)

Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to MacClade,[1] when the authors recognized that implementing a modular architecture in MacClade would be infeasible.[2] Mesquite is largely written in Java and uses NEXUS-formatted files[3] as input. Mesquite is available as a compiled executable for Macintosh, Windows, and Unix-like platforms,[4] and the source code is available on GitHub.

Mesquite: A modular system for evolutionary analysis
Original author(s)Wayne P. Maddison, David R. Maddison
Initial releaseMarch 14, 2001 (2001-03-14)
Stable release
3.2 / January 1, 2017 (2017-01-01)
Repository
Written inJava
Operating systemMacintosh, Windows, Unix-like
PlatformCross-platform
Typescience
Websitemesquiteproject.wikispaces.com

Rationale

The architecture of Mesquite was explicitly designed to exploit the modularity and extensibility of Object-oriented programming.[5] In practice, Mesquite modules are Java classes, usually concrete sub-classes of abstract class definitions.[6] This modular architecture has afforded the development of additional packages[7] that can be used as plug-ins to Mesquite.

Scope

Mesquite provides a number of analyses including ancestral state estimation and diversification analysis. Mesquite also contains tools for simulating data such as species trees, gene trees, and DNA matrices. The base distribution of Mesquite affords interoperability with other programs, for such purposes as multiple sequence alignment (e.g. Clustal and MAFFT), as well as the ability to retrieve DNA sequence data from GenBank. Mesquite includes some rudimentary tools for phylogenetic tree estimation; however, the Zephyr[8] package provides a Mesquite interface for interacting with other phylogenetic inference programs including RAxML,[9][10] PAUP*, and GARLI.

gollark: Better, but it also is designed to run off battery for a while.
gollark: The thing to remember is that laptops have things like "fans" and "actual competent cooling".
gollark: Probably not well except briefly.
gollark: Apple have actually been doing really amazing work, but they still have worse power constraints.
gollark: Don't think so, no.

References
  1. D. R. Maddison & W. P. Maddison. "MacClade". Retrieved 2016-03-11.
  2. Mesquite Project Team. "History of Mesquite". Retrieved 2016-03-11.
  3. Maddison D.R., Swofford D.J., Maddison W.P. (1997). "NEXUS: an extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. ISSN 1063-5157. PMID 11975335.CS1 maint: uses authors parameter (link)
  4. Mesquite Project Team. "Mesquite Installation". Retrieved 2016-03-11.
  5. Mesquite Project Team. "Why Mesquite?".
  6. Mesquite Project Team. "How Mesquite Works". Retrieved 2016-03-11.CS1 maint: uses authors parameter (link)
  7. Mesquite Project Team. "Additional Mesquite Packages". Retrieved 2016-03-11.
  8. Maddison D.R. and Maddison W.P. "Zephyr". Retrieved 2016-03-11.CS1 maint: uses authors parameter (link)
  9. Stamatakis A. "RAxML: Randomized Axelerated Maximum Likelihood". Retrieved 2016-03-11.
  10. Stamatakis A (2014). "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies". Bioinformatics. 30 (9): 1312–1313. doi:10.1093/bioinformatics/btu033. PMC 3998144. PMID 24451623.
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