STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Staden

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

Tandem2 – Automated Microsatellite Allele Binning for Population Genetics Workflows

Tandem2

:: DESCRIPTION

All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. Tandem2 fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units.

::DEVELOPER

Michael Matschiner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Tandem2

:: MORE INFORMATION

Citation

Matschiner M, Salzburger W (2009)
TANDEM: integrating automated allele binning into genetics and genomics workflows.
Bioinformatics, 25(15), 1982-1983.

msatcommander 1.0.8 – Locate Microsatellite Repeats, Design Locus-specific Primers, and Tag ’em

msatcommander 1.0.8

:: DESCRIPTION

msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).

::DEVELOPER

faircloth-lab

:: SCREENSHOTS

msatcommander

:: REQUIREMENTS

  • MacOsX/Windows
  • Python

:: DOWNLOAD

 msatcommander

:: MORE INFORMATION

Citation

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.
Faircloth BC.
Mol Ecol Resour. 2008 Jan;8(1):92-4. doi: 10.1111/j.1471-8286.2007.01884.x.

RepeatSeq v0.8.2 – Genotyping Microsatellite Repeats Tool

RepeatSeq v0.8.2

:: DESCRIPTION

RepeatSeq determines genotypes for microsatellite repeats in high-throughput sequencing data.

:: DEVELOPER

Mittelman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

 RepeatSeq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan 7;41(1):e32. doi: 10.1093/nar/gks981. Epub 2012 Oct 22.
Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
Highnam G1, Franck C, Martin A, Stephens C, Puthige A, Mittelman D.

HighSSR 1.1 – Microsatellites Markers de novo design and Prediction

HighSSR 1.1

:: DESCRIPTION

HighSSR is a microsatellite prediction framework for microsatellite genotyping based on high-throughput sequencing.

::DEVELOPER

Alexander Tchourbanov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HighSSR

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Nov 1;28(21):2797-803. doi: 10.1093/bioinformatics/bts524. Epub 2012 Sep 6.
HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.
Churbanov A1, Ryan R, Hasan N, Bailey D, Chen H, Milligan B, Houde P.

mStruct – Population Genetic Analysis of Microsatellite data

mStruct

:: DESCRIPTION

mStruct is a software for detection of population structure in the presence of admixing and mutations from multi-locus genotype data. It is a mixed membership model (also referred to as an admixture model) which incorporates a mutation process on the observed genetic markers.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 mStruct

:: MORE INFORMATION

Citation

S. Shringarpure and E. P. Xing,
mStruct: Inference of Population Structure in Light of Both Genetic Admixing and Allele Mutations,
Genetics. 2009 Jun;182(2):575-93.

MSA 4.05 – Microsatellite Analyzer

MSA 4.05

:: DESCRIPTION

The MSA software tool was designed to handle large microsatellite data sets. To avoid error prone reformatting, MSA uses a simple input format, very close to a simple spreadsheet.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 MSA

:: MORE INFORMATION

Citation:

Dieringer, Daniel & Schlötterer, Christian (2003)
Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets.
Molecular Ecology Notes 3 (1), 167-169

MSIsensor 0.2 – Microsatellite Instability Detection

MSIsensor 0.2

:: DESCRIPTION

MSIsensor is a C++ program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MSIsensor

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1015-6. doi: 10.1093/bioinformatics/btt755. Epub 2013 Dec 25.
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
Niu B1, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC, Ding L.

MicroErrorAnalyzer 1.0 – Analyse Genotyping Errors of Microsatellites in Parentage Exclusion Analysis

MicroErrorAnalyzer 1.0

:: DESCRIPTION

MicroErrorAnalyzer is a computer program  for analysing the genotyping errors of microsatellites in parentage exclusion analysis.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

 MicroErrorAnalyzer

:: MORE INFORMATION

Citation

Effects of genotyping errors on parentage exclusion analysis.
Wang J.
Mol Ecol. 2010 Nov;19(22):5061-78.

Micro-Checker 2.2.3 – Microsatellite Data Checking Software

Micro-Checker 2.2.3

:: DESCRIPTION

Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies.

::DEVELOPER

Cock van Oosterhout, Bill Hutchinson,Derek Wills and Peter Shipley

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Micro-Checker

:: MORE INFORMATION

Citation

Cock van Oosterhout, Bill Hutchinson,Derek Wills and Peter Shipley
MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data
Molecular Ecology Notes (2004)4, 535–538