Various Utilities for Microbial Genomics and Metagenomics

A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 ).

Installing enveomics.R

To install the latest version of enveomics.R uploaded to CRAN, execute in R:


To install the current developer version of enveomics.R, execute in R:

install_github('lmrodriguezr/enveomics', subdir='enveomics.R')

Using enveomics.R

To load enveomics.R, simply execute:


And open help messages using any of the following commands:


You can run some examples using these libraries in the enveomics-GUI.

For additional information on recruitment plots, see the Recruitment plots working document.


  • 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder initialization to median (instead of mode).
  • 1.4.2: Solved bug #36.
  • 1.4.0: New option pos.breaks.tsv for enve.recplot2.
  • 1.3.4: Gracefully handles and plots recruitment plots with insufficient data to find peaks.
  • 1.3.3: New function enve.recplot2.windowDepthThreshold.
  • 1.3.2: New option for plot.enve.RecPlot2.
  • 1.3.1: New function enve.truncate.
  • 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
  • 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve with S3 methods plot and summary.
  • 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and solved a minor bug in enve.recplot2 that caused failures in low-coverage datasets when using too many threads.
  • 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a bin per subject sequence.


Reference manual

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1.8.0 by Luis M. Rodriguez-R, a year ago

Browse source code at

Authors: Luis M. Rodriguez-R [aut, cre]

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

Artistic-2.0 license

Depends on stats, methods, parallel, fitdistrplus, sn, investr

Suggests tools, vegan, ape, picante, gplots, optparse

See at CRAN