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Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic under- or over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu
This is a submission to PeerJ for review.
List of scripts and functions currently available in the enveomics collection
For an updated categorized list visit http://enve-omics.ce.gatech.edu/enveomics/docs .
Conceptual workflow of the TRIBS algorithm applied to phylogenetic distances
The TRIBS (Transformed-space Resampling In Biased Sets) algorithm is described in the main text. The entire set (i.e., phylogenetic space of genomes or genome-derived features) is represented in black and the selected subset for evaluation (i.e., genomes presenting the trait of interest) is represented in burgundy. Median is abbreviated as Med.