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These software tools may be freely used for all non-commercial purposes.
(c) Copyright, 2017 by Professor Alexander Zelikovsky
Department of Computer Science, Georgia State University
Atlanta, GA 30303 (404) 651-0676
IsoEM 1.1.4 The IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data
xpathway : A set of tools that compares metabolic pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways. The XPathway analysis of pathway activity is based on expectation maximization and topological properties of pathway graphs.
2SNV Quasispecies reconstruction from long reads
ScaffMatch: Scaffolding Algorirthm Based on Maximum Weight Matching
Pooling: Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling
VGA: Viral Genome Assembler is a method for accurate assembly of a heterogeneous viral population coupled with a high-fidelity sequencing protocol able to eliminate errors from sequencing data.
kGEM k-Genotype Expectation Maximization algorithm for Reconstructing a Viral population from Single-Amplicon reads
VirA/VirA-MCF reconstruct viral quasipecies and estimate their frequencies from amplicon reads.
IsoEM: Infers isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
KEC Error correction for pyrosequencing reads (454 Life Sciences and Ion Torrent)
MaLTA : Transcriptome assembly and quantification from RNA-Seq reads
ViSpA: Viral Spectrum Assembler implements a novel viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via Expectation Maximization on all reads.
2SNP: SCALABLE PHASING METHOD BASED ON 2-SNP HAPLOTYPES. New phasing is based on statistically significant LD and deviation from Hardy-Weinberg equilibrium. On datasets across 69 regions from HapMap 2SNP is 3-4 orders of magnitude faster and usually outperforms HAPLOTYPER, GERBIL and matches PHASE.
Please, contact alexz@cs,gsu,edu regarding older software tools below:
MetNetAligner: Web service tool for
- matching metabolic pathways/networks
- identifying pathway holes (missing enzymes) and suggesting plausible candidates
- and finding network motifs
DACS: Disease Association Combinatorial Search software searches for statistically significant multi-SNP combinations associated with a disease.
Tagging: Tag Selection based on SNP Multivariate Linear Regression.
Disease Association: This project explores disease susceptibility prediction on genotype/haplotype data.
Trio Phasing: Frequently case/control genotype data represents family trios consisting of two parents and one offspring. The trio phasing project develops a satisfactory method for phasing family trio data.