MSTMap protocols

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MSTMap specifications

Information


Unique identifier OMICS_07416
Name MSTMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Unique identifier OMICS_07416
Name MSTMap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for MSTMap

MSTMap in pipelines

 (4)
2017
PMCID: 5422545
PMID: 28536597
DOI: 10.3389/fpls.2017.00765

[…] markers were combined with 733 polymorphic snp markers previously genotyped using illumina goldengate 1536 snp array (). combined snp marker segregation data were used for linkage analysis using mstmap. snp markers from the goldengate assay served as anchor markers to identify additional snp loci within the targeted qtls. all the snp markers identified within qtls were converted to kasp […]

2017
PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] for having >90% similarity with another ril. markers with segregation distortion were identified and any markers with a p-value < 1e-10 were removed. genetic maps were constructed using the mstmap.cross function. the p-value cutoff for genetic map construction (with and without imputation) was adjusted so that 10 or more distinct linkage groups were identified, and the detection of bad […]

2014
PMCID: 4083584
PMID: 25071835
DOI: 10.3389/fgene.2014.00208

[…] (iv) integrate the wgs snps and assembly contigs harboring them (figure )., the popseq method () utilizes established software for read mapping (bwa (), variant calling [samtools ()] and map-making [mstmap ()]. snps detected by whole-genome sequencing of a mapping population are placed into a genetic framework of this same population through a simple nearest neighbor search. popseq was first […]

2013
PMCID: 4298792
PMID: 23998490
DOI: 10.1111/tpj.12319

[…] alleles; in the absence of heterozygous calls, this corresponds to a minimum minor allele frequency of 17.6%. for m × b, 4058 snps passed these filters. genetic map construction was performed using mstmap () with the following parameters: population type dh; distance function kosambi; cut_off_p_value 0.00001; no_map_dist 20; no_map_size 2; missing_threshold 0.8; estimation_before_clustering no; […]


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MSTMap in publications

 (85)
PMCID: 5908840
PMID: 29674702
DOI: 10.1038/s41598-018-24349-4

[…] les and duplicated lines were also removed. only snps that were polymorphic in both the parents and the ril population, and had minor allele frequencies (mafs) >0.25 were used for linkage mapping. mstmap (http://www.mstmap.org/) was used for genetic map construction, with the following parameters: grouping lod criteria = 10; population type = dh (doubled haploid); no mapping size threshold = 2; […]

PMCID: 5905146
PMID: 29665794
DOI: 10.1186/s12870-018-1267-8

[…] by the pearl millet genome sequencing consortium). filtering for high quality polymorphic snps reduced the number of snps to 2416, which were used in the first step of the map construction. the mstmap algorithm grouped all snps in 7 linkage groups (lgs), except 73 outlying snps, which were excluded. the grouping of lgs agreed with the grouping of the reference genome sequence. the 2343 snps […]

PMCID: 5828438
PMID: 29485999
DOI: 10.1371/journal.pone.0192261

[…] dh population that was previously used to construct a ssr-based genetic map []. the complete dataset of 13,378 markers was employed for map construction using the software package mstmap [], which was further refined in mapdisto software [] as described by fowler et al. []. markers with ≥10% missing data and incorrectly genotyped by not following parental alleles were removed […]

PMCID: 5895680
PMID: 29372282
DOI: 10.1007/s00122-018-3055-0

[…] were calculated separately for both populations. only snps with a minor allele frequency of at least 30% and missing rate below 10% were considered for map construction. linkage maps were built with mstmap (wu et al. ) using the population type ‘ril8’ and a cut-off p value of 10−12. correctness of the maps was assessed by comparison to the popseq reference map (mascher et al. ) using r scripts […]

PMCID: 5793172
PMID: 29304028
DOI: 10.3390/genes9010019

[…] to good dh lines (93), clearly segregating for 1:1 ratio, were used for genetic linkage mapping., high-quality snp markers were used to construct linkage maps in two steps. in the first step, mstmap software (version 2.0) []—available freely at github—was used to construct draft maps. following thresholds/parameters were used for computation: (i) kosambi mapping function [], (ii) […]


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MSTMap institution(s)
Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA

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