Mapping Software
Autozygosity mapping
This set of web pages contains programs that analyse Affymetrix SNP chip data files for regions of IBD. AutoSNPa concentrates on files
from groups of individuals that are assumed to have the same haplotype. Where as IBDfinder makes no assumptions about haplotypes and can
screen individuals from different ethnic groups as well as data from different SNP microarray datasets. Sample requires data from a number
of nuclear familes and while each of the nuclear families doesn't have to have a common haplotype, all the families must have mutations in
the same gene. The main feature of Sample is that it doesn't require genotype data from affected people, just the parents and siblings of
affected individuals. this makes it possible to analyse embroyonic lethal mutations.
- AutoSNPa is a program that analysis SNP data from pedigrees with multiple affected
individuals.
- AutoSNPa is a program designed to display an individual's autozygous regions next to an
ideogram of the human genome.
- IBDelphi is a program for identifying segments of IBD between two individuals and calculating the risk that
a couple will have a child affected by a autosomal recessive disease.
- IBDfinder analysis SNP data from affected individuals from different pedigree who
have novel mutations in the same gene.
- The Inbreeding calculator page contains a link to two programs. C2T converts a Cyrillic
file to a text file, which can then be imported in to the CofI program to calculate the
coefficient of inbreeding of members of the pedigree. Since CofI can use any suitably formatted
pedigree the program was also used a the basis of a web page with the same functionality.
- SAMPLE is a program that identifies homozygous regions linked to a disease phenotype,
but unlike AutoSNPa and Ibdfinder, it does not require data from affected individuals.
Dominant Mapping
This set of programs is designed to map genes with a dominant mode of inheritance.
- DominantMapper, this program was created to map disease genes that show a dominant
mode of inheritance in related nuclear families.
- PoD, this program was developed to identify regions linked to a dominant disease
gene using SNP data from pooled DNA samples. However the method does not seem to
work.
Copy number analysis
This program is designed to map genes which are affected by variations in copy number.
- CNViewer, this program was created to map copy number variation that is common to affected
individuals, but absent from health individuals.
Mapping file formating software
The section contains applications that convert different genotyping file formats to those that the software on this page can use.
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