UCLA Human Genetics Software Distribution

For researchers in the Dept. of Human Genetics: please visit the software list for information on software available on our servers (e.g., calypso).

Mendel v13.2

(expires 1 May 2014)

Comprehensive Package for Exact Statistical Genetic Analysis of Qualitative and Quantitative Traits.

README :: Online Docs :: Download

Mendel Impute 2012

Software for performing genotype imputation by solving matrix completion problems [3, 7, 2] over a sliding window of SNPs.

Online Docs :: Download

Vintage Mendel

Ken Lange's vintage statistical genetics software developed prior to 2000. Mendel 3.3.5 is still used when compiling SimWalk 2.91.

Download

SimWalk2 v2.91

Stochastic Statistical Analysis of Qualitative Traits. Available analyses include: Haplotyping, Parametric Linkage, Non-Parametric Linkage (NPL), Identity-by-Descent (IBD), and Mistyping. SimWalk2 analyzes large pedigrees using MCMC estimation techniques.

README :: Online Docs :: Download

MicroMerge v2.00

Software for merging microsatellite genotype data sets.

README :: Online Docs :: Download

Vocabulon v1.0

Identification of conserved words in DNA sequence

README :: Online Docs :: Download

Autoscan

AUTOSCAN automatically creates data files, uses MAKEPED (converts pre-linkage format files to linkage format), DOWNFREQ (estimates allele frequencies from pedigree data), and PEDCHECK (Mendelian checking) programs and finally starts statistical analyses via the ANALYZE package. ANALYZE performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,the disease model file, the number of loci file, and the ANALYZE input file.The AUTOSCAN also allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.

Visit the Autoscan site

Generic Genetic Studies Database

The Generic Genetic Studies Database (GGSD) is an open-source, web-integrated and relational database driven data management software package for large scale genetic studies.

Visit the GGSD site

Admixture

A program for fast maximum likelihood estimation of individual ancestry based on multilocus SNP genotypes

Visit the Admixture site