Tag: Marker

EH 24 – Estimate Linkage Disequilibrium between Different Markers

EH 24

:: DESCRIPTION

EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous “disease” (case-control) option has been deleted (but see below how to work with case-control data).

::DEVELOPER

Lab of Statistical Genetics, Rockefeller University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 EH

:: MORE INFORMATION

References

Marchini J et al (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78, 437-450

Xie X, Ott J (1993) Testing linkage disequilibrium between a disease gene and marker loci. Am J Hum Genet 53, 1107 (abstract)

Terwilliger J, Ott J (1994) Handbook of Human Genetic Linkage. Johns Hopkins University Press, Baltimore

CSI – Construct Confidence set of Markers within prespecified Genetic Distance from the Disease Locus

CSI

:: DESCRIPTION

CSI (confidence set inference) uses affected sib pairs data and relative risks to construct a confidence set of markers within a prespecified genetic distance from the disease locus.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CSI

:: MORE INFORMATION

Citation

Papachristou, C., Lin, S. (2006)
Microsatellites Versus Single-Nucleotide Polymorphisms in Confidence Interval Estimation of Disease Loci.
Genetic Epidemiology, 30, 3-17.

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.

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.

ADMIXMAP 3.8.3103 – Model Admixture using Marker Genotype data

ADMIXMAP 3.8.3103

:: DESCRIPTION

ADMIXMAP is a general-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus.

::DEVELOPER

Paul McKeigue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ADMIXMAP

:: MORE INFORMATION

Citation

Design and analysis of admixture mapping studies.
Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM.
Am J Hum Genet. 2004 May;74(5):965-78. Epub 2004 Apr 14.

GeneArtisan 1.1 – Simulation of Markers in Case-Control Study Designs

GeneArtisan 1.1

:: DESCRIPTION

GeneArtisan: Simulation of Markers in Case-Control Study Designs.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

 GeneArtisan

:: MORE INFORMATION

Citation

Y. Wang and B. Rannala. 2005.
In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection.
American Journal of Human Genetics 76:1066-1073.

Record 2.0 – Arranging Markers into Linear Order

Record 2.0

:: DESCRIPTION

RECORD (REcombination Counting and ORDering) can be used for the ordering of loci on genetic linkage maps. The method minimises the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling.

Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map.

RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes, according to the two-way pseudo-testcross method. Please provide the data in a .LOC file in JoinMap format.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 RECORD

:: MORE INFORMATION

Citation

RECORD: a novel method for ordering loci on a genetic linkage map.
Van Os H, Stam P, Visser RG, Van Eck HJ.
Theor Appl Genet. 2005 Dec;112(1):30-40. Epub 2005 Oct 14. Erratum in: Theor Appl Genet. 2006 Jan;112(2):389.

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