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Protocols

Mesquite specifications

Information


Unique identifier OMICS_08828
Name Mesquite
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format Nexus, Newick, neXML (via plugin module)
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 3.03
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Mesquite_(software)

Versioning


No version available

Mesquite citations

 (844)
library_books

Trabecular architecture in the sciuromorph femoral head: allometry and functional adaptation

2018
PMCID: 5954450
PMID: 29785282
DOI: 10.1186/s40851-018-0093-z

[…] n (Fig. ) is based on a previous study [] and complemented with species from the TimeTree database [] (Gliridae, Tamiops swinhoei, Tamiops rodolphii, Aplodontia rufa, Heliosciurus rufobrachium) using Mesquite version 3.04 []. Given the apparent correlation of the lifestyle categories with the phylogeny (see Fig. ), we conducted subsequent analyses with phylogenetically informed methods. […]

library_books

Ceftazidime Is the Key Diversification and Selection Driver of VIM Type Carbapenemases

2018
MBio
PMCID: 5941070
PMID: 29739906
DOI: 10.1128/mBio.02109-17

[…] hyml/ (PhyML), https://github.com/ddarriba/jmodeltest2 (jModeltest), http://darwin.uvigo.es/rdp/rdp.html (RDP), http://tree.bio.ed.ac.uk/software/ (BEAST/Tracer/FigTree), http://mesquiteproject.org/ (MESQUITE), and http://www.fluxus-engineering.com/ (Network). Moreover, the data sets generated and/or analyzed during the current study are available from the corresponding author on reasonable reques […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] replications. We also examined the phylogenetic distribution of structural changes using the tree constructed with parsimony and ML methods implemented in the ancestral state reconstruction tools of Mesquite 3.2 []. Major genomic changes were binary coded () and mapped on phylogenetic trees. Phylogenetic trees were visualized and edited with TreeGraph2 []. […]

library_books

New data on Amynodontidae (Mammalia, Perissodactyla) from Eastern Europe: Phylogenetic and palaeobiogeographic implications around the Eocene Oligocene transition

2018
PLoS One
PMCID: 5905962
PMID: 29668673
DOI: 10.1371/journal.pone.0193774

[…] unable to show unambiguous synapomorphies in ACCTRAN optimization, whereas PAUP* version 4.0a159 depicted them accurately. This version was then used to visualize transformations, as well as TNT and Mesquite version 3.2 []. The complete list of transformations is provided in .Suprageneric relationships within Rhinocerotoidea are divergent from other recent phylogenies, especially concerning the H […]

library_books

Coexistence of Multiple Endemic and Pandemic Lineages of the Rice Blast Pathogen

2018
MBio
PMCID: 5885030
PMID: 29615506
DOI: 10.1128/mBio.01806-17

[…] oplasy is expected to predominate in outbreeding populations. Homoplastic sites were identified by mapping mutations onto the total evidence genome genealogy with the Trace All Characters function of Mesquite (), applying ancestral reconstruction under the maximum parsimony optimality criterion. The resulting matrix of ancestral states for all nodes was then processed with a python script to deter […]

call_split

Evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates

2018
BMC Evol Biol
PMCID: 5883405
PMID: 29614975
DOI: 10.1186/s12862-018-1166-5
call_split See protocol

[…] models tested []. We performed PGLS to account for the non-independence of the data due to the shared evolutionary history of species. To do that, we constructed a phylogeny for the 196 species using Mesquite 3.04 [] based on the relations at the species-level []. We followed a method described by Martins and Garland [] to set branch lengths to 1 and used Mesquite 3.04 to reconstruct the ancestral […]

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