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bioinformatics:public
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Virus Lab, a.k.a. Sullivan Lab - The Ohio State University
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Tucson Marine Phage Lab's Public Script Repository
Script packages
Data packages
Tucson Marine Phage Lab's Public Script Repository
Script packages
Sequence Analysis Toolkit
A set of general scripts to deal with sequence file format conversion, recruitment plot or synteny plot.
Population Genomics
These scripts are designed to study genetic variability within a given phage population.
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell genomics and metagenomics
This package includes the script used in
Roux, S., Hawley, A.K., Torres Beltran, M., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S.J., Sullivan, M.B. (doi:10.7554/eLife.03125). Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell genomics and metagenomics
.
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
This includes the scripts used in
Deng, L., Ignacio-Espinoza, J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (doi:10.1038/nature13459). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature.
The Pacific Ocean Virome (POV)
This package includes the scripts used in
Hurwitz, B.L., & Sullivan, M.B. (2013). The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8(2), e57355.
Quantitative assessment of concentration, purification and replication in viral metagenomics
This package includes the scripts used in
Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 15(5), 1428–1440.
Phylogenomics of T4 cyanophages: Lateral gene transfer in the 'core' and origins of host genes.
This includes the scripts used in
Ignacio-Espinoza, J.C., & Sullivan, M.B. (2012). Phylogenomics of T4 cyanophages: Lateral gene transfer in the 'core' and origins of host genes. Environ Microbiol. 14(8), 2113-2126.
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes.
This package includes the script used in Roux, S., Hallam, S.J., Woyke, T., Sullivan, M.B. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes.
Data packages
taxonomy_data.zip
iplantsampledata.zip
bioinformatics/public.txt
· Last modified: 2015/10/15 22:37 (external edit)
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