msatcommander protocols

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
Requirements BioPython, wxPython
Maintained Yes



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  • person_outline Brant Faircloth <>

Publication for msatcommander

msatcommander IN pipelines

PMCID: 4850052
PMID: 27144104
DOI: 10.3732/apps.1500110

[…] dna library sequencing resulted in 15,243 reads of 32–662 bp. we found 572 contigs of 60–660 bp using clc genomics workbench version 5.5 (qiagen). microsatellite motifs were found in 533 reads using msatcommander (faircloth, 2008). many microsatellite motifs had repeats that were either too long or too short or comprised single base pair repeats. primer3 (koressaar and remm, 2007; untergasser et […]

PMCID: 4915918
PMID: 27347451
DOI: 10.3732/apps.1500143

[…] (clc bio, aarhus, denmark) produced 81,275 contigs (word size 43, bubble size 40, n50: 502 bp)., microsatellite regions (≥10 dinucleotide repeats, ≥7 trinucleotide repeats) were searched using msatcommander (faircloth, 2008). primer pairs with an optimal annealing temperature of 60 ± 2°c, a gc content of 30–70%, and a product size range of 100–500 bp were generated by primer3 (rozen […]

PMCID: 4948900
PMID: 27437172
DOI: 10.3732/apps.1600020

[…] benchtop sequencer (illumina) in 2 × 300-bp read mode. the data were assembled into contigs in fastq-join software (aronesty, 2011). microsatellite regions were mined among contigs of >400 bp in msatcommander version 1.0.8 software (faircloth, 2008). the search parameter was restricted to dinucleotide motifs with a minimum of 16 repeats. primer pairs for microsatellite amplification […]

PMCID: 5033367
PMID: 27672523
DOI: 10.3732/apps.1600056

[…] into contigs in fastq-join software (aronesty, 2011), resulting in a total of 1,738,214 contigs. contigs were screened using primer3 version 2.2.3 software (rozen and skaletsky, 1999) embedded in msatcommander version 1.0.8 software (faircloth, 2008) to identify dinucleotide motifs with a minimum of 15 repeats. consequently, a total of 5049 primer pairs were designed. in the amplification […]

PMCID: 4542945
PMID: 26312198
DOI: 10.3732/apps.1500045

[…] run de novo assembly (parameters used: mismatch cost 3, insertion and deletion cost 2, length fraction 0.5, similarity fraction 0.9), resulting in 63,448 contigs with an n50 length of 1348 bp. using msatcommander (faircloth, 2008), we screened the contigs including microsatellite regions for ≥6 dinucleotide repeats and ≥4 tri- to hexanucleotide repeats. a total of 138 primer pairs were designed […]

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.

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