Genome Sequencing, Assembly, and Browser Tools

• Smapper
  
  Solexa Read Mapper
• Cyrene - cis-Lexicon and cis-Browser
  
  A database and genome browser for cis-regulatory information
• Ariadne
  
  A browser for processing population genomics workflows
• Assembly Simulator
  
  A genome assembly simulator written in Mathematica

SNPs, Haplotypes, and GWAS

• HAPCOMPASS: A fast algorithm for accurate haplotype assembly
  
  Given a set of aligned sequence reads in a SAM file and a set of variant calls in VCF format, HAPCOMPASS will assemble reads into haplotypes
• DELISHUS: An algorithm for detecting deletions in shared haplotypes using SNPs
  
  An algorithmic framework for finding inherited and de novo deletions in a GWAS SNP dataset consisting of trios or pairs
• Long-range Trio-Phaser
  
  A long-range haplotype phasing tool developed for GWAS SNP datasets consisting of trios
• Imperfect Ancestral Recombination Graph (iARG)
  
  A collection of tools to reconstruct evolutionary histories which include recombination and back/recurrent mutation events

Integrated Environments for Biology

• Cellarium
  
  An integrated framework for genome browsers and bioinformatics workflows
• Virtual Sea Urchin
  
  4D Map of the purple sea urchin developmental process

Education and Classroom Tools

• Genomathica
  
  A library of Mathematica tools and software for bioinformatics education and simulation. Genomathica is currently under construction in preparation for its first release.

Other Bioinformatics Tools

• ProFOLDING
  
  Discrete models and algorithms for protein folding
• Cancer Diagnosis
  
  An automated algorithm to determine the level of malignancy of images of tumor biopsies