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Protocols

MSTRAT specifications

Information


Unique identifier OMICS_20079
Name MSTRAT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format ASCII
Operating system Unix/Linux, Windows
Computer skills Advanced
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Brigitte Gouesnard

Publication for MSTRAT

MSTRAT citations

 (20)
call_split

An informational view of accession rarity and allele specificity in germplasm banks for management and conservation

2018
PLoS One
PMCID: 5831390
PMID: 29489873
DOI: 10.1371/journal.pone.0193346
call_split See protocol

[…] lle richness, were used to compare these core subsets with other generated by the state-of-the-arte methods called replica exchange Monte Carlo (REMC) [], parallel mixed replica exchange (MixRep) and MSTRAT []. Although the method employed in [] for a core subset selection from the same wheat collection is not a direct optimization, but a stratified sampling strategy [], an additional subset of 1, […]

library_books

Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini Core Collection Using DArTseq

2017
Front Plant Sci
PMCID: 5651524
PMID: 29093721
DOI: 10.3389/fpls.2017.01748

[…] g et al., ), including the random and stratified sampling methods that require subgroups created based on a priori knowledge (Brown, ); the maximization of the allelic diversity/richness method using MSTRAT (Gouesnard et al., ), Core Hunter (Thachuk et al., ; Beukelaer et al., ) and principal component scoring (Noirot et al., ); and the distance-based methods, such as Core Hunter, MLST (Perrier et […]

call_split

Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

2017
Front Plant Sci
PMCID: 5591941
PMID: 28928752
DOI: 10.3389/fpls.2017.01463
call_split See protocol

[…] ine and 48 single sequence repeat (SSR) primers, spread across each of the eight subterranean clover chromosomes, were selected from the results of to identify the most diverse lines. Analysis using MSTRAT software () to optimize maximum diversity within the minimum number of lines, resulted in an optimum core collection of 97 lines, covering 80.1% of the genetic diversity within the whole subter […]

library_books

Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World

2017
Front Plant Sci
PMCID: 5526916
PMID: 28798757
DOI: 10.3389/fpls.2017.01296

[…] seed size (100-seed weight >40 g), 23.3% of medium size (100-seed weight 25–40 g) and 3.3% of small size (100-seed weight < 25 g) (Supplementary Table ).With the standard M strategy as implemented in MSTRAT (Gouesnard et al., ), five nested core subsets (sample size: 10, 15, 20, 25, 30) were first built. Next, the advanced M strategy as implemented in PowerCore v1.0 (Kim et al., ) allowed the sele […]

library_books

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

2016
BMC Genet
PMCID: 5109817
PMID: 27842492
DOI: 10.1186/s12863-016-0452-8

[…] to be a useful method in selecting a core set conserving high genetic diversity with a reasonable size []. There are two representative core selection methods implementing the M strategy, namely the MSTRAT algorithm [] and PowerCore software []. Here, we used the advanced M strategy as implemented in PowerCore 1.0 software and successfully established a representative core collection with high ge […]

call_split

Utilization of Molecular, Phenotypic, and Geographical Diversity to Develop Compact Composite Core Collection in the Oilseed Crop, Safflower (Carthamus tinctorius L.) through Maximization Strategy

2016
Front Plant Sci
PMCID: 5069285
PMID: 27807441
DOI: 10.3389/fpls.2016.01554
call_split See protocol

[…] MSTRAT (Gouesnard et al., ) and POWERCORE (Kim et al., ) were used for development of independent core collections using phenotypic data of seasons 2011–12, 2012–13 and genotypic data reported by Kuma […]

Citations

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MSTRAT institution(s)
INRA-SGAP, Centre de Montpellier, Domaine de Melgueil, Mauguio, France; INRA, Station de Génétique Végétale, Gif sur Yvette, France; Department of Biology, McGill University, Montreal, Quebec, Canada
MSTRAT funding source(s)
Supported by the French Ministère de l’Agriculture and Bureau des Ressources Génétiques; by the National Science and Engineering Research Council of Canada and by INRA.

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