CHANGES

Version 1.5.0

  • now the NAST algorithm trims candidate sequences to that which is bound by the beginning and end points of the alignment span; with the the new option –nast-notrim in micca msa produces the same results of the previous version (<=1.4.0)

Version 1.4.0

  • nofilter option added to micca.api.msa.nast() (do not remove positions which are gaps in every sequenceces) and to the msa command (–nast-nofilter option);
  • Documentation improved.

Version 1.3.0

  • Swarm clustering algorithm added to micca otu;
  • micca.api.otu.denovo_swarm() function added;
  • micca v1.3.0 includes: VSEARCH v1.9.5, MUSCLE v3.8.31, FastTree v2.1.8, swarm v2.1.8.
  • Minor: Documentation updated.

Version 1.2.2

  • Fix: now micca can generate plots with matplotlib when DISPLAY environment variable is undefined;
  • Minor: MANIFEST.in, Dockerfile updated.

Version 1.2.1

  • Dockerfile added;
  • Documentation improved.

Version 1.2.0

  • Hits output file option added to micca.api.msa.nast() (hits_fn option) and to the msa command (–nast-hits option);
  • Improved setup.py.

Version 1.1.0

  • strand option added in ‘classify’ (consensus-based classifier), ‘msa’ (NAST) and ‘otu’ (closed-reference and open reference OTU picking protolcols) commands. Now these commands search both strand (default) instead the plus strand only.

Version 1.0.0

  • micca 1.0.0 includes: VSEARCH v1.9.5, MUSCLE v3.8.31, FastTree v2.1.8.