UCLA Human Genetics Software Distribution

Mendel v14.2 and v14.3

(1 July 2015)

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

Admixture

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

Visit the Admixture site

ConvexCluster

CONVEXCLUSTER is an implementation of convex clustering, a principled clustering method that is appropriate for dynamically inferring clusters in a manner similar to standard hierarchical clustering. In contrast to hierarchical clustering however, convex clustering is more accurate, robust to outliers, and versatile. As for versatility, convex clustering allows users to specify weights informed by expert domain knowledge and a desired level of granularity. CONVEXCLUSTER includes code written in OpenCL so that users with nVidia or ATI GPUs can run convex clustering efficiently on high dimensional data. The program is currently available as beta and can be checked out from our Google Code repository with a SVN client from the link below. Please submit any questions regarding usage, bugs. etc. to the link below via the Issue tracker on the Google Code repository.

Visit the CONVEXCLUSTER site

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