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Finds phylogenetic relatedness to be strongest predictor of microbial co-occurrence (explains about 10% of the variance in microbial co-occurrence). Kamneva_2016 is a method that introduces two new genome-wide pairwise measures of microbe-microbe interaction. The first (genome content similarity index) quantifies similarity in genome composition between two microbes, while the second (microbe-microbe functional association index) summarizes the topology of a protein functional association network built for a given pair of microbes and quantifies the fraction of network edges crossing organismal boundaries.

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Kamneva 2016 specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
Python
Stability:
Stable
Source code URL:
https://github.com/olgakamneva/Kamneva_2016
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced

Credits

Publications

Institution(s)

Department of Biology, Stanford University, Stanford, CA, USA

Funding source(s)

This work was supported by a National Institutes of Health grant RO1GM117590 and by the National Science Foundation NSF DBI-1458059.

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