genomics2ecology R package
This is an R package which allows to compute genome content similarity and micorbe-microbe functional association indices, genome level summaries which in general are correlated with co-occurrence of microbial species inferred from 16S rRNA data.
Download: [GitHub].
Publication: Kamneva. Submitted.

Making consensus cluster network from rooted gene trees
This is an R script which takes a list of rooted gene trees, wich can be multilabeles, for instance gene trees rooted using outgroup species, threshold value at which to consider reticulations, threshold value for bootstrap support in input trees and produces species cluster network which then can be visualized in Dendroscope program.
Download: coming soon.
Publication: Kamneva et al. (in preparation)

Data from paper "Genome composition of microbes predicts their co-occurrence in the environment"
This is the dataset accompanying paper in submission. Please read README.txt file for details on the content.
Download: [Dropbox]
Publication: Kamneva. Submitted.

Signal peptides in proteins from 99 bacterial genomes and gene families linked to intracellular membranes
This is the dataset accompanying published paper but can be mined for various things. The dataset includes signal peptides scans for proteins from 99 distantly related microbial genomes, summary gene family information. Please read README.txt file for details on the content.
Download: [Dropbox]
Publication: Kamneva et al. PLoS ONE. 2015.

Dated species tree for 99 bacterial genomes, genome and gene family information
This is the dataset accompanying published paper but can be mined for various things. The dataset includes over 15,000 protein families (alignments, gene trees and gene tree species tree reconciliation information obtained with AnGST program) from 99 distantly related microbial genomes and species tree dated with PhyloBayes. Please read README.txt file for details on archive content.
Download: coming soon.
Publication: Kamneva et al. GBE. 2012.