Third-Party Tools

• GeneTree
  GeneTree estimates mutation, migration and growth rates, and ancestral inference such as the time to the most recent common ancestor of a sample of DNA sequences.
• Genotype graphing tool
  Contributed by Mr. Yechiel Lamash (email: hilik@tx.technion.ac.il)
  This MatLab code takes a PharmGKB genotype excel file and plots genotype vs. PharmGKB ID. Documentation
• Godzilla
  A pipeline for real-time comparative analysis of the human and mouse genomes. Given either a FASTA sequence or the RefSeq gene name, Godzilla's zBrowser will respond with a VISTA graph of the human-mouse comparison.
• Goodness-of-fit for a Locus Showing Departure from Hardy-Weinberg Equilibrium
  This tool inputs the genotype counts in affected cases and unaffected controls that show a departure from HWE and outputs the best-fit disease model to the observed data.
• HAPLO
  The HAPLO, HAPLO/PERMUTE, and related programs estimate frequencies of multi-site haplotypes using the EM algorithm. Written in VAX Fortran for DEC VAX systems running VMS 6.2.
• MAXDIP
  Maxdip is an application to estimate a reciprocal recombination (cross-over) rate parameter (rho) and a gene conversion rate parameter (f) from population variation data.
• Paralleled DHSMAP Software This is an enhanced version of DHSMAP designed for high performance computers and computer clusters.
• PHASE
  PHASE is a program for reconstructing haplotypes.
• PolyPhred
  PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred, Phrap and Consed. PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. PolyPhred documentation and tutorial are available online.
• PromoLign
  PromoLign provides graphical presentation for SNPs and transcription factor binding sites in the promoter region of genes in the context of human-mouse orthologous sequence alignment. It is designed to help identify potential regulatory motifs in the upstream sequence of a gene and to evaluate the function of SNPs in this region.
• RECSLIDER
  RECSLIDER is a program that calculates the population recombination (cross-over) rate parameter rho (4Nr) per bp from population variation data over a "sliding window".
• SPLOSH
  This S-plus code computes estimates of the false discovery rate (FDR) at each p value in a large set of p values resulted from testing a large number of statistical hypotheses. It can be used to conduct FDR-based error assessment for statistical inference in genome-wide studies where a large number of hypotheses are tested, such as microarray gene differential expressions, trait-marker association analysis using large number of SNPs or SNP microarrays, and genotype-phenotype association analysis involving a large number of loci or phenotypes.
• Statistical Explanation for Positional Cloning - stepc
  Stepc is an implementation of the method discussed in the paper "A Statistical Method for Identification of Polymorphisms that Explain a Linkage Result" (2002) American Journal of Human Genetics70:399-411.
• TAMAL
  Open source tool to select single nucleotide polymorphisms (SNPs) for genotyping based on haplotype tag and SNPs with several different predicted functions.