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MLSTest specifications

Information


Unique identifier OMICS_25405
Name MLSTest
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.1.23
Stability Stable
Source code URL https://archive.codeplex.com/?p=mlstest
Maintained Yes

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Maintainer


  • person_outline Nicolas Tomasini

Publication for MLSTest

MLSTest citations

 (11)
library_books

Estimating the Intra taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii

2018
Front Genet
PMCID: 5928140
PMID: 29740480
DOI: 10.3389/fgene.2018.00148

[…] and the lowest nucleotide diversity (0.002); whereas for C. gatti, VGII presented the highest number of haplotypes (147), while the lowest diversity was presented in VGIV (Supplementary Table ).Using MLSTest software, parameters were calculated to establish the utility of the markers used in the MLST including the number of polymorphisms, the TE, and the DP. The results showed higher TE levels for […]

call_split

Multilocus sequence typing: genetic diversity in Trypanosoma cruzi I (TcI) isolates from Brazilian didelphids

2018
PMCID: 5824584
PMID: 29471851
DOI: 10.1186/s13071-018-2696-9
call_split See protocol

[…] of individual diplotypes and haplotypes, and also to determine the best combination and minimum combination of loci that enable identification of the maximum number of diploid sequence types (DSTs). MLSTest software [] was initially applied to calculate the typing efficiencies (TE) and discriminatory power (DP) for each target. TE is defined as the number of identified genotypes divided by the nu […]

call_split

Genetic variation analysis and relationships among environmental strains of Scedosporium apiospermum sensu stricto in Bangkok, Thailand

2017
PLoS One
PMCID: 5507518
PMID: 28704511
DOI: 10.1371/journal.pone.0181083
call_split See protocol

[…] 33710, KU533657, KU533716, KU533698, and KU533717. Each sequence was trimmed to the correct length with the start and the end of each gene (shown in ). Genotype variation of each gene was analyzed by MLSTest v1.0.1.23 software, which was downloaded from http://ipe.unsa.edu.ar/software []. The ATs number was created by using the same software and allele profiles were used to assign the STs number. […]

library_books

Evaluation of a Multilocus Sequence Typing (MLST) scheme for Leishmania (Viannia) braziliensis and Leishmania (Viannia) panamensis in Colombia

2017
PMCID: 5429539
PMID: 28499458
DOI: 10.1186/s13071-017-2175-8

[…] The results from MLSTest showed a total of seven DSTs for L. braziliensis and five DSTs for L. panamensis (due to the lack of a DST database, the DSTs detected were included in Additional file : Tables S1, S2). Based […]

library_books

Importation of Hybrid Human Associated Trypanosoma cruzi Strains of Southern South American Origin, Colombia

2016
PMCID: 4982185
PMID: 27434772
DOI: 10.3201/eid2208.150786

[…] loci ( Table 3) (); and 10 mitochondrial gene fragments (). Diploid multilocus sequence typing (MLST) data were analyzed by locus and concatenated according to their relative chromosomal positions in MLSTest (); heterozygous variable sites were handled as average states. Gene haplotypes were inferred using PHASE version 2.1 (). PCR products were cloned and sequenced to confirm ambiguous gene phase […]

call_split

Bats, Trypanosomes, and Triatomines in Ecuador: New Insights into the Diversity, Transmission, and Origins of Trypanosoma cruzi and Chagas Disease

2015
PLoS One
PMCID: 4605636
PMID: 26465748
DOI: 10.1371/journal.pone.0139999
call_split See protocol

[…] hat resembles the GTR-G model, but it is optimized for faster performance [].Also, to test the combinability of the 18S rRNA and cytb genes for concatenated phylogenetic analysis we used the software MLSTest [] to run the analysis ILD-BIONJ [] that is an efficient variant of the incongruence length difference test []. We ran ILD-BIONJ with reduced alignments that only contained strains represented […]

Citations

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MLSTest institution(s)
Unidad de Epidemiologia Molecular (UEM), Instituto de Patologia Experimental, Universidad Nacional de Salta-CONICET, Salta, Argentina; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Wales, Bangor, UK

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