The software tools here were developed in the Zhang lab over many years by grant support from NSF, NIH, The Alzheimer's Association and Monsanto Corporation.

Computational Biology

AmpSeq-SSR
An accurate and efficient method for large-scale SSR genotyping and applications (software, supplemental table)
miRvial
A computational method and software package for detecting and characterizing microRNAs of diverse genomic origins (software)
BlocBuster
An allele-specific and network-based GWAS method (paper1, paper2, software)
mgRF
Module-guided Random Forests for integration of genotypic variation and gene expression for analyzing complex traits (paper, software)
miRank
MicroRNA prediction with a novel ranking algorithm based on random walks (paper, software and data files)
Qcut and HQcut
Finding communities in networks; also with scripts for visualizing clustering results and for constructing and clustering gene co-expression networks (paper1, paper2, software)
WordSpy
A steganalysis-based, genome scale motif finding method (software)
Rearrangement clustering
A method with application to gene expression analysis (paper, software)
DBTree
A bi-directional regression tree approach to modeling transcriptional regulation (paper, software)
Iterated loop matching
A method for RNA folding with pseudonots (software)
Degenerate multiple PCR primers
A method for selecting degenerate multiple PCR primers (software)

Optimization and Search

Cut-and-solve for the ATSP
MaxSolver
An exact max-SAT solver (software)
Backbone guided WalkSAT
A method with dynamic noise strategy for SAT and Max-SAT (software)