To request software or assistance with technical issues, please email istrail.lab@gmail.com and Derek Aguiar rap@cs.brown.edu
Tractatus
- Exact and subquadratic algorithm for IBD inference.
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
cis-Browser
- A genome browser for cis-regulatory information
- inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
cis-Lexicon
- A database for cis-regulatory information
- sea urchin developmental gene regulatory networks
- building a high-resolution transcriptome map of the embryo
- inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
CLOSE
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
Virtual Sea Urchin
- 4D Map of the purple sea urchin developmental process
Ariadne
- A browser for processing population genomics workflows
Cancer Diagnosis
- An automated algorithm to determine the level of malignancy of images of tumor biopsies
Viral Immunology and Comparative
Immunopeptidomics of Humans and their Pathogens
ProFOLDING
- Discrete models and algorithms for protein folding
- Graph Theory of Self avoiding Walks
- Contact Maps and Protein Structure
- Energy Function Inference
- PDB Structure Alignment
- Lattice Protein Folding Algorithms with mathematically guaranteed Error Bound
Assembly Simulator
- A genome assembly simulator written in Mathematica
Genomathica
- A library of Mathematica tools and software for bioinformatics education and simulation.
- Genomathica is currently under construction in preparation for its first release.