Changes for version 0.1.8 - 2016-01-08

  • Script bc_relative_to_absolute will now round results if requested
  • IdConverter can now append or prepend in addition to replacing IDs
  • More robust FormatGuesser
  • Extended detection of generic file format
  • Handling of relative abundances in unifrac file format
  • Much faster Sampler tool, courtesy of the Math::GSL modules
  • All random number duties relegated to Math::GSL
  • Speed optimizations in Community module


Create species accumulation curves (collector or rarefaction)
Add a taxonomic lineage to community members
Remove low-count, low-prevalence community members
Merge/split community files and convert between formats
Convert member ID from member attribute or file
Try fixing incorrect taxonomic assignments, using a reference community
Get information about a community file
Delete or rename community members
Include, delete, merge, sort or rename samples
Measure alpha diversity of communities
Measure beta diversity between communities
Rarefy communities
Convert relative abundances into absolute
Remove community members not expected to occur, based on a reference community
Summarize community composition


A biological community
Calculate the alpha diversity of a community
Read and write files that describe communities
Driver to read and write files in the sparse BIOM format
Dummy driver (does nothing)
Driver to read and write files in the GAAS format
Driver to read and write files in a generic tab-delimited site-by-species table format
Driver to read and write files in the QIIME format
Driver to read and write files in the (Fast)Unifrac format
Determine the format used by a community file
The basic constituent of a biological community
A metacommunity, or group of communities
Beta diversity or distance separating communities
Calculate the gamma diversity of a metacommunity
Role for objects that have a taxonomic classification
Role for objects that have a description
Role for IO layer
Role for objects that can be locked (made read-only)
Role for objects that use a pseudo-random number generator
Role for objects that have a sequence
Role to read/write data tables and provide random access to their cells
Role for objects that have a weight
Functions for manipulating taxonomic lineages
Species accumulation curves
Various methods to convert member ID
Normalize communities by count
Sample organisms according to their abundance
Remove low-count, low-abundance community members
Create a summary of communities
Arbitrary transformation of member counts
Data type definitions