msatcommander statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool msatcommander

Tool usage distribution map

This map represents all the scientific publications referring to msatcommander per scientific context
info info

Associated diseases

This word cloud represents msatcommander usage per disease context

Popular tool citations

chevron_left Conventional primer design Microsatellite detection chevron_right
Want to access the full stats & trends on this tool?


msatcommander specifications


Unique identifier OMICS_16541
Name msatcommander
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data The DNA sequence data in single-sequence or concatenated.
Input format FASTA
Output data A summary file, the locus-specific primers.
Output format CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Medium
Version 1.0.8
Stability Stable
BioPython, wxPython
Maintained Yes




No version available



  • person_outline Brant Faircloth

Publication for msatcommander

msatcommander citations


Characterization of tri and tetra nucleotide microsatellite loci for the freshwater snails Promenetus exacuous (Planorbidae) and Valvata tricarinata (Valvatidae) and their utility in population genetic studies

BMC Res Notes
PMCID: 5870918
PMID: 29587859
DOI: 10.1186/s13104-018-3301-1
call_split See protocol

[…] Torrent PGM system with each species allocated approximately 25% of a 318 chip. Raw genomic data were converted to FASTA format using Geneious ver. 8.1 []. Microsatellite motifs were identified using msatcommander 1.0.8 []. Parameters were set to search for perfect tri- and tetranucleotide repeats with a minimum length of eight repeat units to decrease the potential for genotyping errors due to st […]


High Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

Front Genet
PMCID: 5855144
PMID: 29593777
DOI: 10.3389/fgene.2018.00073

[…] previously generated by shotgun genome sequencing of P. costatus and deposited in the database of the Laboratory of Biotechnology and Molecular Markers were used for in silico analysis. The software msatcommander () was used to identify microsatellite regions. Over 100,000 contigs containing microsatellite regions were identified, and about 1,000 primer pairs suggested. We screened the primer pai […]


Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing

Front Genet
PMCID: 5827183
PMID: 29520294
DOI: 10.3389/fgene.2018.00046
call_split See protocol

[…] Enzyme code (EC), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis through the Bi-directional Best Hits (BBH) method.Microsatellites were identified in the contigs using msatcommander software (Faircloth, ). Primers flanking the microsatellite loci were designed with Primer3plus software (Rozen and Skaletsky, ). The six possible reading frames of the consensus sequenc […]


Development and evaluation of 16 new microsatellite loci for the rock ptarmigan (Lagopus muta) and cross species amplification for the willow grouse (L. lagopus)

BMC Res Notes
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] e of 120 base pair (bp), a match percentage of 94% and a minimum sequence length of 150 bp. From this dataset all di-, tri-, tetra-, penta- and hexanucleotides repeats were screened with the software msatcommander [, ] and sequences less than 100 bp and/or with a small number of repeats were excluded. Primers were designed with Primerselect software (part of the Lasergene package []). Every micros […]


Assessment of intra and interregional genetic variation in the Eastern Red backed Salamander, Plethodon cinereus, via analysis of novel microsatellite markers

PLoS One
PMCID: 5650168
PMID: 29053730
DOI: 10.1371/journal.pone.0186866

[…] tional sequencing employed the 454 GS FLX titanium sequencing kit XL+ (Roche) run on ½ 70 x 75 mm picotiter plate.To identify 454 fragments that contained potentially amplifiable loci (PALs), we used MSATCOMMANDER 1.0.8 [] to scan for repeat containing fragments. When running these searches, we required that dinucleotide and trinucleotide motifs contain ≥ eight repeat units and that tetra-hexanucl […]


Isolation and characterization of microsatellite markers for Hypochaeris incana (Asteraceae) and close relatives1

Appl Plant Sci
PMCID: 5664967
PMID: 29109922
DOI: 10.3732/apps.1700081

[…] ; National Center for Biotechnology Information [NCBI] Sequence Read Archive BioProject no. PRJNA314301). The methodology for primer development followed with slight modifications as outlined below. MSATCOMMANDER version 0.8.2 () identified 2466 sequences with microsatellite motifs with the following options: di-, tri-, and tetranucleotide repeats ≥6 repeat units, combine multiple arrays within a […]

Want to access the full list of citations?
msatcommander institution(s)
D. B. Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA, USA
msatcommander funding source(s)
Supported by the Tall Timbers Research Station and Land Conservancy’s Quail Research Initiative, Daniel B. Warnell School of Forestry and Natural Resources, UGA, McIntyre-Stennis projects GEO-0100-MS and GEO-0136-MS, and the UGA Institute of Ecology.

msatcommander reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review msatcommander