MPR statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

MPR specifications

Information


Unique identifier OMICS_08818
Name MPR
Alternative name Most Parsimonious Reconciliation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jean-Philippe Doyon

Publication for Most Parsimonious Reconciliation

MPR citations

 (8)
library_books

GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

2018
BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] k, the reconciliation score corresponds to the probability density of the gene tree given some parameters (rates of events and branch lengths) under a birth-death and gain model of evolution. For the Most Parsimonious Reconciliation model (MPR), this score corresponds to the optimal number of gene gain and loss events, weighted by their costs, explaining the incongruence between a gene tree and a […]

library_books

Probabilistic inference of lateral gene transfer events

2016
BMC Bioinformatics
PMCID: 5123345
PMID: 28185583
DOI: 10.1186/s12859-016-1268-2

[…] Goodman et al. [] introduced the notion of a tree reconciliation, which took duplication and loss of genes into account. They used a parsimony based approach and proposed an algorithm that finds the most parsimonious reconciliation (MPR) in the presence of gene duplication and gene loss events. The most parsimonious reconciliation is a reconciliation that uniquely maps the vertices of a gene tree […]

library_books

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality

2015
BMC Bioinformatics
PMCID: 4647304
PMID: 26573665
DOI: 10.1186/s12859-015-0803-x

[…] atio cost vector; r m: the lower bound of the ratio cost vector; v(e): the event count vector of the event e; v(α): the event count vector of the reconciliation α; c o s t m(G,S ′,c): the cost of the most parsimonious reconciliation between S ′ and G with respect to the cost vector c; […]

library_books

Improved gene tree error correction in the presence of horizontal gene transfer

2014
Bioinformatics
PMCID: 4393519
PMID: 25481006
DOI: 10.1093/bioinformatics/btu806

[…] ecently been proposed for gene families with transfer. Both work by considering alternative gene tree topologies, reconciling them to the species tree and choosing the gene tree that yields the best (most parsimonious) reconciliation. AnGST accounts for uncertainty in gene tree topologies by taking as input, not a single gene tree, but a set of gene trees (e.g. bootstrap replicates) and creating a […]

call_split

Joint amalgamation of most parsimonious reconciled gene trees

2014
Bioinformatics
PMCID: 4380024
PMID: 25380957
DOI: 10.1093/bioinformatics/btu728
call_split See protocol

[…] Here, we consider the problem of finding the most parsimonious reconciliation (MPR) when considering—as possible macro-events that result in the birth and death of gene copies—speciation, gene duplication, gene transfers and gene loss (). The ge […]

library_books

A Bayesian Supertree Model for Genome Wide Species Tree Reconstruction

2014
Syst Biol
PMCID: 4851173
PMID: 25281847
DOI: 10.1093/sysbio/syu082

[…] mented as well, taking advantage of our solution to the normalization constant. An example of a promising distance would be one based on the recently developed DLCpar algorithm (), which can find the most parsimonious reconciliation scenario by considering duplications, losses, and deep coalescences at once. Another option would be based on algorithms for finding the minimum cost reconciliation in […]

Citations

Looking to check out a full list of citations?

MPR institution(s)
LIRMM, CNRS - Université Montpellier 2, France; Center for Bioinformatics (ZBIT), Tuebingen University, Germany; Kharkevich IITP, Russian Academy of Sciences, Moscow; LBBE, CNRS - Université Lyon 1, France; ISEM, CNRS - Université Montpellier 2, France
MPR funding source(s)
This work was funded by the ANR-08-EMER-011 project.

MPR reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MPR