GMATA v2.3 – Genome-wide Microsatellite Analyzing Toward Application

GMATA v2.3

:: DESCRIPTION

GMATA is an easiest and fastest bioinformatic tool /software for any Simple Sequence Repeats (SSR) analyses, and SSR marker designing, polymorphism screen, and e-mapping in any DNA sequences.

::DEVELOPER

Xuewen Wang

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java
Perl

:: DOWNLOAD

GMATA

:: MORE INFORMATION

Citation

Wang X, Wang L.
GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.
Front Plant Sci. 2016 Sep 13;7:1350. doi: 10.3389/fpls.2016.01350. PMID: 27679641; PMCID: PMC5020087.

GMATo 1.2 – Genome Microsatellite Analyzing Tool

GMATo 1.2

:: DESCRIPTION

GMATo is a novel soft for faster and accurate microsatellite mining at any length and comprehensive statistical analysis for DNA sequences in any genome at any size, with easily customized parameters control for biologists and bio-informatician, running easily at common computers with Windows, Linux, MAC OS etc multiple platforms (platform independently) with both graphic and command interface programmed in Java and Perl computing language.

::DEVELOPER

Xuewen Wang

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java
Perl

:: DOWNLOAD

GMATo

:: MORE INFORMATION

Citation

Bioinformation. 2013 Jun 8;9(10):541-4. doi: 10.6026/97320630009541. Print 2013.
GMATo: A novel tool for the identification and analysis of microsatellites in large genomes.
Wang X1, Lu P, Luo Z.

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

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.

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.

MSIsensor 0.6 – Microsatellite Instability Detection

MSIsensor 0.6

:: 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.

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

HighSSR team

:: 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.

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

:: 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.

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

EVOINFORMATICS GROUP

:: 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.

RepeatHMM v2.0.3 – Estimation of Repeat Counts on Microsatellites from long-read sequencing data

RepeatHMM v2.0.3

:: DESCRIPTION

RepeatHMM is a novel computational tool to detect any microsatellites (including trinucleotide repeats in trinucleotide repeat disorders (TRD)) from given long reads for a subject of interests. It is able to accurately estimate estimate expansion counts according to the evaluation performance on both simulation data and real data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

RepeatHMM

:: MORE INFORMATION

Citation

Liu Q, Zhang P, Wang D, Gu W, Wang K.
Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing.
Genome Med. 2017 Jul 18;9(1):65. doi: 10.1186/s13073-017-0456-7. PMID: 28720120; PMCID: PMC5514472.