A data set of 38 host-phage infection matrices that were collected and presented in the article Statistical structure of host–phage interactions. Each excel datasheet represents a different study. Rows represent hosts and columns phages. One cells represents infection and zero cells no-infection.
A collection of Perl scripts to calculate gene-level similarity among annotated genomes as used in Kislyuk et al. BMC Genomics 12: 32 (2011). The scripts can be executed from the command line and the only dependencies are BioPerl and NCBI BLAST. Separately, we include a MATLAB script to calculate fluidity and its variance directly from matrices of shared and total gene counts.
The article "Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems" was published in Plant Physiology on January 27, 2010.
Click here to read the full version of the article.
To learn more about the project goals and our collaborators go to the RootNet website.
Here you can download the images used for root trait analysis:
An R package accompanies our 2010 paper on fluctuation domains. The package includes the source code for simulations and R scripts that create each of the figures in the paper. This can be used to re-run simulations shown in the paper with different parameter values to explore how each influences the onset of fluctuations. Currently only tested on a Linux machine with GNU Standard Library (GSL) installed. The source code is now released on DRYAD using the Creative Commons public domain license.
LikelyBin is an unsupervised metagenomic binner. The binner application is written in Perl and C and is tested to run on Linux distributions. The releases are available below.
If you use LikelyBin, please cite:
- Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff and Joshua S. Weitz. Unsupervised Statistical Clustering of Environmental Shotgun Sequences. BMC Bioinformatics 2009, 10:316.