Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to
MacClade, when the authors recognized that implementing a modular architecture in MacClade would be infeasible. Mesquite is largely written in
Java
Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...
and uses
NEXUS
NEXUS is a joint Canada Border Services Agency and U.S. Customs and Border Protection-operated Trusted Traveler and expedited border control program designed for pre-approved, low-risk travelers. Members of the program can avoid waits at border ...
-formatted files as input. Mesquite is available as a compiled executable for Macintosh, Windows, and Unix-like platforms, and the source code is available on
GitHub
GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...
.
Rationale
The architecture of Mesquite was explicitly designed to exploit the modularity and extensibility of
Object-oriented programming
Object-oriented programming (OOP) is a programming paradigm based on the concept of '' objects''. Objects can contain data (called fields, attributes or properties) and have actions they can perform (called procedures or methods and impl ...
. In practice, Mesquite ''modules'' are Java
classes, usually concrete sub-classes of abstract class definitions. This modular architecture has afforded the development of additional packages 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
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...
(e.g.
Clustal
Clustal is a computer program used for multiple sequence alignment in bioinformatics. The software and its algorithms have gone through several iterations, with ClustalΩ (Omega) being the latest version . It is available as standalone software, ...
and
MAFFT
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version used an algorithm based on multiple seq ...
), as well as the ability to retrieve DNA sequence data from
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...
. Mesquite includes some rudimentary tools for
phylogenetic tree estimation; however, the Zephyr package provides a Mesquite interface for interacting with other phylogenetic inference programs including RAxML,
, and GARLI.
External links
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References
{{Reflist
Phylogenetics software