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Home > Lab Software Tools

Lab Software Tools

To request software or assistance with technical issues, please email [email protected] and Derek Aguiar [email protected]

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.