Tag: Genetic Distance

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.

DistMiss 1.0 – Compute Matrix of Genetic Distances between Populations

DistMiss 1.0

:: DESCRIPTION

DistMiss computes a matrix of genetic distances between populations on the basis of their allele frequencies at L loci.

::DEVELOPER

DistMiss Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Fortran

:: DOWNLOAD

 DistMiss

:: MORE INFORMATION

DISPAN – Genetic Distance and Phylogenetic Analysis

DISPAN

:: DESCRIPTION

DISPAN (Genetic Distance and Phylogenetic Analysis) computes (1) average heterozygosity and its standard error for each population, (2) gene diversity (Ht) and its associate parameters, Hs, and Gst (Nei 1973), (3) standard genetic distances (D) between populations (Nei 1972), (4) standard errors of standard genetic distances (Nei 1978), (5) DA distances between populations (Nei et al. 1983). It also constructs phylogenetic trees by using the neighbor-joining (NJ) method (Saitou and Nei 1987) and the unweighted pair group-method with arithmetic mean (UPGMA) (Sneath and Sokal 1973) from matrices of either D or DA distances. Bootstrap tests (Efron 1982, Felsenstein 1985) for these trees can be performed

::DEVELOPER

Tatsuya Ota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  DISPAN

:: MORE INFORMATION

GeneticDistances 20090824 – Calculate common Genetic Distances for Allele Frequency data

GeneticDistances 20090824

:: DESCRIPTION

GeneticDistances is a program for my graduate students that calculates theta, Ds, and Da for genetic data in GENEPOP format

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 GeneticDistances

:: MORE INFORMATION

DISTANCE – Plot Genetic Distances between Populations

DISTANCE

:: DESCRIPTION

DISTANCE uses an evolutionary algorithm to find suitable placings on a 2-dimensional surface. Genetic distances between populations (or between individuals) are supplied in your text file.

::DEVELOPER

Brian  Kinghorn.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DISTANCE

:: MORE INFORMATION

Citation

Kinghorn, B.P. and Shepherd, R.K. 2001.
A graphic display of genetic distances between populations.
Assoc. Advmt. Anim. Breed. Genet. 14: 273-276.