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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

QUASIM QUAsispecies SIMulator software for viral population evolution with immune response

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.