Software

Software

Metagenomics

 

Omega: http://omega.omicsbio.org

Haider, T.-H. Ahn, B. Bushnell, J. Chai, A. Copeland, and C. Pan. (2014) Omega: an Overlap-graph de novo Assembler for Metagenomics, Bioinformatics 30, 2717-2722.

 

Sigma: http://sigma.omicsbio.org

T-H. Ahn, J. Chai, and C. Pan. (2015) Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance, Bioinformatics 31, 170-177.

 

Phylogenomics

 

UniFam: http://unifam.omicsbio.org

J. Chai, G. Kora, T.-H. Ahn, D. Hyatt, and C. Pan. (2014) Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam, BMC Evolutionary Biology 14.

 

Proteomics

 

Sipros Ensemble: http://sipros.omicsbio.org

X. Guo, Z. Li, Q. Yao, R.S. Mueller, J.K. Eng, D.L. Tabb, W.J. Hervey, C. Pan. (Accepted) Sipros Ensemble improves database searching and filtering for complex metaproteomics, Bioinformatics
Y. Wang, T.H. Ahn, Z. Li, C. Pan, Sipros/ProRata: a versatile informatics system for quantitative community proteomics. Bioinformatics 29, 2064-2065, doi:10.1093/bioinformatics/btt329 (2013).

 

ProRata: http://prorata.omicsbio.org

C. Pan, G. Kora, W. H. McDonald, and e. al. (2006) ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation, Analytical Chemistry 78, 7121-7131.

 

Metabolomics

 

MIDAS: http://midas.omicsbio.org

Y. Wang, G. Kora, B. P. Bowen, and C. Pan. (2014) MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics, Analytical Chemistry 86, 9496-9503.