DetSel 1.0.3 – Detect Markers Responding to Selection

DetSel 1.0.3

:: DESCRIPTION

DetSel is an R package to detect markers responding to selection

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 DetSel

:: MORE INFORMATION

Citation

J Hered. 2003 Sep-Oct;94(5):429-31.
DetSel 1.0: a computer program to detect markers responding to selection.
Vitalis R1, Dawson K, Boursot P, Belkhir K.

mOTUs 2.5.1 – Tool for Marker Gene-based OTU (mOTU) Profiling

mOTUs 2.5.1

:: DESCRIPTION

The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

mOTUs

:: MORE INFORMATION

Citation

Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese, et al.
Nature Communications 10, Article number: 1014 (2019): https://doi.org/10.1038/s41467-019-08844-4

MendelSoft 0.9.8 – Detect Marker Genotyping Incompatibilities

MendelSoft 0.9.8

:: DESCRIPTION

MendelSoft is an open source software which detects marker genotyping incompatibilities (Mendelian errors only) in complex pedigrees using weighted constraint satisfaction techniques. The input of the software is a pedigree data with genotyping data at a single locus. The output of the software is a list of individuals for which the removal of their genotyping data restores consistency. This list is of minimum size when the program ends.

::DEVELOPER

Simon De Givry, BIA, INRA, Toulouse, France @ The Division of Applied Mathematics and Informatics(MIA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 MendelSoft

:: MORE INFORMATION

Citation

M. Sanchez, S. de Givry, and T. Schiex
Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques
In Constraints journal, special issue on bioinformatics, 13(1), 2008.

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.

pSTR Finder – Discover Polymorphic Short Tandem Repeat Markers from Whole-genome Sequences

pSTR Finder

:: DESCRIPTION

pSTR Finder is freely available as a means of identifying putative polymorphic short tandem repeat (STR) loci from data generated from genome-wide sequences.

::DEVELOPER

pSTR Finder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences.
Lee JC, Tseng B, Ho BC, Linacre A.
Investig Genet. 2015 Aug 5;6:10. doi: 10.1186/s13323-015-0027-x.

GIST 0.3 – Detect Association between Marker Genotypes and IBD sharing at the same locus

GIST 0.3

:: DESCRIPTION

The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus.  Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially).  The software can be used to analyze affected sibship data.

::DEVELOPER

Chun Li

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

GIST

:: MORE INFORMATION

Citation

Li C, Scott LJ, Boehnke M. (2004)
Assessing Whether an Allele Can Account in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431

Gene Stacker 1.8 – Marker-assisted Gene Pyramiding

Gene Stacker 1.8

:: DESCRIPTION

Gene Stacker is a flexible open source tool for marker-assisted gene pyramiding. It can be used to construct efficient crossing schedules that gather desired alleles residing in multiple individuals into a single, specific target genotype (the so-called ideotype).

::DEVELOPER

Herman De Beukelaer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 Gene Stacker

:: MORE INFORMATION

Citation

BMC Genet. 2015 Jan 30;16(1):2.
Heuristic exploitation of genetic structure in marker-assisted gene pyramiding problems.
Beukelaer H, Meyer G, Fack V.

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.

OptDis – Subnetwork Markers Package

OptDis

:: DESCRIPTION

OptDis is a novel network-based classification algorithm using color coding technique to identify optimally discriminative subnetwork markers.

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OptDis

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 1;27(13):i205-13. doi: 10.1093/bioinformatics/btr245.
Optimally discriminative subnetwork markers predict response to chemotherapy.
Dao P1, Wang K, Collins C, Ester M, Lapuk A, Sahinalp SC.

KinInfor v1 – Calculate Informativeness of Markers in Inferring Pairwise Relatedness

KinInfor v1

:: DESCRIPTION

KinInfor (Kinship Informativeness) is a Fortran program that calculates the informativeness of markers in inferring pairwise relatedness or relationships.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

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

:: DOWNLOAD

  KinInfor

:: MORE INFORMATION

Citation

Wang, J (2006)
Informativeness of genetic markers for pairwise relationship and relatedness inference.
Theoretical Population Biology 70:300-321.