Tag: Marker

QMSIM 1.10 – Qtl and Marker SIMulator

QMSIM 1.10

:: DESCRIPTION

QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.

::DEVELOPER

Mehdi Sargolzaei , Flavio Schenkel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 QMSim

:: MORE INFORMATION

Citation

Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045

ADMIXMAP 3.8.3103 – Model Admixture using Marker Genotype data

ADMIXMAP 3.8.3103

:: DESCRIPTION

ADMIXMAP (Admixture mapping)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

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

  ADMIXMAP

:: MORE INFORMATION

Citation:

Carcinogenesis. 2011 Mar;32(3):312-7. Epub 2010 Nov 29.
Admixture mapping of lung cancer in 1812 African-Americans.
Schwartz AG et al.

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.

Gene Stacker 1.9 – Marker-assisted Gene Pyramiding

Gene Stacker 1.9

:: 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

Gene Stacker team

:: 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.

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

ATOM – Association Test via Optimally-weighted Markers

ATOM

:: DESCRIPTION

ATOM is a software of powerful gene-based Association Test by combining Optimally Weighted Markers within a genomic region. Due to variation in linkage disequilibrium, different markers often associate with the trait of interest at different levels.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ATOM

:: MORE INFORMATION

Citation

Li M, Wang K, Grant SF, Hakonarson H, Li C (2009)
ATOM: A powerful gene-based association test by combining optimally weighted markers.
Bioinformatics 25:497-503 (PMID: 19074959)

 

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.

OptDis – Optimally Discriminative Subnetwork Biomarkers

OptDis

:: DESCRIPTION

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

::DEVELOPER

Phuong Dao

:: 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.

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.

CITE-sort – Artificial-cell-type Aware Surface Marker Clustering method for CITE-seq data

CITE-sort

:: DESCRIPTION

CITE-sort conducts auto-gating with CITE-seq ADT data using recursive Gaussian Mixture Model. It is robust against artificial cell types that stem from multiplets. CITE-sort also provides concrete explanations of its internal decision process by constructing a biologically meaningful sort tree.

::DEVELOPER

Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

CITE-sort

:: MORE INFORMATION

Citation

Lian Q, Xin H, Ma J, Konnikova L, Chen W, Gu J, Chen K.
Artificial-cell-type aware cell-type classification in CITE-seq.
Bioinformatics. 2020 Jul 1;36(Suppl_1):i542-i550. doi: 10.1093/bioinformatics/btaa467. PMID: 32657383; PMCID: PMC7355304.