Tag: Mapping

disentangler 20111001 – Linkage Disequilibrium Mapping and Haplotype Analysis

disentangler 20111001

:: DESCRIPTION

The disentangler is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers.

::DEVELOPER

Kumasaka Natsuhiko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 disentangler

:: MORE INFORMATION

Citation

N. Kumasaka, Y. Okada, A. Takahashi, M. Kubo, Y. Nakamura and N. Kamatani.
Disentangler: a visualization technique for linkage disequilibrium mapping using multi-allelic loci ;
(Abstract / Program #708F). Presented at the 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics, October 14, 2011, Montreal, Canada.

ASPEX 2.5 – Affected Sib-pair Exclusion Mapping

ASPEX 2.5

:: DESCRIPTION

ASPEX is a set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits.There are five main analysis programs: sib_ibd, sib_phase, sib_map, sib_tdt, and sib_kin.

  • sib_ibd performs exclusion mapping for data sets with typed parents, and makes no inferences about missing data.
  • sib_phase performs exclusion mapping using allele frequencies to reconstruct missing information, and is tailored for data sets with missing parents, but additional typed children that can be used to reconstruct and phase the parents.
  • sib_map is for multipoint marker distance estimation from sib pair data.
  • sib_tdt is for transmission disequilibrium testing.
  • sib_kin is for verifying the degree of relatedness of individuals within a family.

::DEVELOPER

David Hinds, dahinds@users.sourceforge.net 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASPEX

:: MORE INFORMATION

Citation:

Genet Epidemiol. 1999;17 Suppl 1:S187-91.
Sib-pair analysis of the collaborative study on the genetics of alcoholism data set.
Jorgenson E, Hinds D, Risch N.

GRAMA 1.1 – Genetic Recombinant Analysis & Mapping Assistant

GRAMA 1.1

:: DESCRIPTION

GRAMA (Genetic Recombinant Analysis and Mapping Assistant) is a new tool that automates TGCE data analysis for genetic mapping purpose. Data from multiple TGCE runs are integrated and displayed in an intuitive visual format. GRAMA includes its own algorithm to detect peaks in electropherograms, and peaks detected by GRAMA are automatically compared with those of another software package for any difference that will be flagged for user inspection. Analyses of the automatically combined genetic mapping results from GRAMA reveal high accuracy with virtually zero errors. Because of the accuracy of the calls and the intuitive interface, GRAMA boosts user productivity more than two-fold relative to previous manual methods.

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS


:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • JAVA

:: DOWNLOAD

Registration First ; GRAMA

:: MORE INFORMATION

Citation

GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis data. Philip M. Maher, Hui-Hsien Chou, Elizabeth Hahn, Tsui-Jung Wen and Patrick S. Schnable. Theoretical and Applied Genetics Online First, April 2006. DOI: 10.1007/s00122-006-0282-6