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HyperPolymorphism: hypergeometric-based analysis of polymorphisms in
nucleotide sequences
 HyperPolymorphism is a simple tool for comparing sequences obtained from
two pooled samples in order to identify single nucleotide polymorphism (SNP)
and insertion/deletion (indel) alleles that are
differentially represented in each pool. HyperPolymorphism
does this by assuming a hypergeometric distribution
of alleles between the two samples (similar to Fisher’s exact test). The
input of HyperPolymorphism consists of two pileup
files generated using SAMtools (http://samtools.sourceforge.net/cns0.shtml),
each file representing the compact alignment of sequences obtained from one
of the pooled samples. The output of HyperPolymorphism
is two tab-delimited files, ranking the SNPs and indels
based on differential representation of their alleles in the two samples.
HyperPolymorphism is a part of HyperGenometrics
which will be released soon. HyperGenometrics will
allow analysis of a much wider range of data types, including microarray data
and phylogenetic profiles, with the final goal of
facilitating functional genomics.
HyperPolymorphism Developers:
Hamed Shateri Najafabadi
Reza Salavati
Last updated on 5/16/2011 9:00:30 PM
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