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MP-EST specifications

Information


Unique identifier OMICS_06053
Name MP-EST
Alternative name Maximum Pseudo-likelihood for Estimating Species Trees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_06053
Name MP-EST
Alternative name Maximum Pseudo-likelihood for Estimating Species Trees
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Maximum Pseudo-likelihood for Estimating Species Trees

MP-EST citations

 (45)
library_books

Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave making behaviour

2018
BMC Evol Biol
PMCID: 5872393
PMID: 29592795
DOI: 10.1186/s12862-018-1159-4

[…] this grouping is unambiguous and maximal in all the phylogenies constructed in our study (100 in the three RAxML Maximal likelihood analyses, 1.0 for the PhyloBayes Bayesian inference and 100 for the MP-EST shortcut coalescence approach). This result contrasts with previous studies that failed to retrieve a high bootstrap support for the monophyly of the temporary social parasite clade [, ]. Copto […]

library_books

Delimiting Coalescence Genes (C Genes) in Phylogenomic Data Sets

2018
Genes
PMCID: 5867844
PMID: 29495400
DOI: 10.3390/genes9030123

[…] nts that mark the boundaries of these units. C-genes are the basic unit of analysis for most coalescence methods that are used to infer species trees with summary coalescence methods such as STAR [], MP-EST [], NJst [], and ASTRAL-II []. Indeed, a basic assumption of these coalescence methods is that recombination occurs freely among c-genes but not within c-genes. When sequence evolution is compl […]

library_books

Rooting phylogenetic trees under the coalescent model using site pattern probabilities

2017
BMC Evol Biol
PMCID: 5738147
PMID: 29258427
DOI: 10.1186/s12862-017-1108-7

[…] e issue in species tree inference. Some coalescent inference methods, such as ASTRAL, do not directly infer the root of the estimated species phylogeny [, ]. Still other coalescent inference methods (MP-EST, NJst) require rooted gene trees as the input in order to estimate a rooted species tree [, ]. However, ancestor (rooting) identification is essential for complete understanding of the evolutio […]

library_books

Expanded Taxonomic Sampling Coupled with Gene Genealogy Interrogation Provides Unambiguous Resolution for the Evolutionary Root of Angiosperms

2017
Genome Biol Evol
PMCID: 5710718
DOI: 10.1093/gbe/evx233

[…] e based on the alternative sets of gene trees obtained. The ASTRAL-II v 4.10.12 (; ) analyses used unrooted gene trees with multilocus bootstrapping () and local posterior probability support (). The MP-EST () analyses used rooted gene trees and multilocus bootstrapping support (24 gene trees were discarded for MP-EST as they lacked outgroups for tree rooting after excluding S.moellendorffii). Fin […]

library_books

Coalescent Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons

2017
Mol Biol Evol
PMCID: 5850733
PMID: 29087487
DOI: 10.1093/molbev/msx277

[…] re likely to match the true gene tree (): for example, found that use of bootstrapped gene trees led to deteriorated performance by astral.We also inferred species trees from the ML gene trees using mp-est 1.5 (). The mp-est method estimates species tree from a set of rooted gene trees by maximizing a pseudo-likelihood, which is the probability of the three alternative gene trees given a triplet […]

call_split

Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation

2017
BMC Evol Biol
PMCID: 5580441
PMID: 28863778
DOI: 10.1186/s12862-017-1047-3
call_split See protocol

[…] ing a bootstrap algorithm with 1000 replicates. The resulting tree was visualized in FigTree v1.4.2 []. We performed species tree reconstructions using the maximum pseudo-likelihood coalescent method MP-EST [] implemented in the STRAW [] webserver, as well as a Bayesian method implemented in *BEAST v1.8.2 []. The anonymous locus q25 could not be sequenced for E. fallax and hence was removed from s […]

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MP-EST institution(s)
Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, USA

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