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.

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

IMEx 2.0 – Imperfect Microsatellite Extractor

IMEx 2.0

:: DESCRIPTION

IMEx is a tool for extracting Perfect, Imperfect and Compound Microsatelites or Simple Sequence Repeats (SSR’s) or Short Tandem Repeats (STR’s) from genome sequences.

::DEVELOPER

IMEx Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

IMEx

:: MORE INFORMATION

Citation

Suresh B. Mudunuri and Hampapathalu. A. Nagarajaram (2007)
IMEx: Imperfect Microsatellite Extractor.
Bioinformatics 23(10):1181-1187.

MISA – MIcroSAtellite Identification Tool

MISA

:: DESCRIPTION

MISA (MIcroSAtellite Identification Tool) allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.

::DEVELOPER

Thomas Thiel @ the Plant Genome Resources Center (PGRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/ MacOSX
Perl

:: DOWNLOAD

MISA

:: MORE INFORMATION

Citation

Theor Appl Genet. 2003 Feb;106(3):411-22. Epub 2002 Sep 14.
Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).
Thiel T, Michalek W, Varshney RK, Graner A.

YCDMA 3.1.1 – Manage Microsatellite Data

YCDMA 3.1.1

:: DESCRIPTION

YCDMA (Y Chromosome Data Management) is designated to manage microsatellite data (mono- and bi-allelic).In order to reflect the hierarchical organization of an experiment, samples may be arranged into user-defined populations and populations into groups.Data defined in an experiment may be exported in one of the following formats (allowing their use in the corresponding softwares) :

ARLEQUIN
DISPAN
GENEPOP
MICROSAT
MIGRATE
NJBAFD

::DEVELOPER

Daniel Montagnon PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

YCDMA

:: MORE INFORMATION

If you download and use this software please register to be informed for new release and modifications.

MicroMerge 2.0 – Merge Microsatellite Genotype Data Sets

MicroMerge 2.0

:: DESCRIPTION

MicroMerge automates merging of microsatellite data sets that were genotyped at different facilities or using different protocols or platforms. The software employs a Bayesian statistical model that matches allele frequencies between data sets (Presson et al. 2006). MicroMerge v2.0 enables the following aspects of control: 1) output file formats which can be handled by most statistical genetic analysis packages, 2) tailoring the algorithm to different merging scenarios, such as data sets with very different sample sizes or multiple data sets, 3) merging small data sets when a reliable set of allele frequencies are available, and 4) improving the quantity and 5) quality of merged data.

::DEVELOPER

Angela P. Presson (micromerge@genetics.ucla.edu), UCLA Human Genetics

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

MicroMerge

:: MORE INFORMATION

Citation:

Angela P Presson , Eric M Sobel , Paivi Pajukanta , Christopher Plaisier , Daniel E Weeks , Karolina Åberg and Jeanette C Papp (2008)
Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis
BMC Bioinformatics 2008, 9:317