LCAClassifier v3.2.2

Minor release fixing bug that did not allow floats to be used for bitscore percentage dropoff

LCAClassifier v3.2.1

Minor release fixing potential installation issue (biopython and setuptools)

LCAClassifier v3.2.0

Major release adding BOLD for classification of COI (mitochondrial cytochrome c oxidase I) amplicons. Also fixes installation problem caused by python2 incompability of numPy.

Not previously advertised, LCAClassifier now supports the calculation of biotic quality indexes (option -a)

LCAClassifier v3.1.0

Major release including improved version of SilvaMod128:

1. parts of SILVA sequences falling outside the SSU rRNA gene were removed using the SILVA alignment. This previously may have caused biases with some eukaryotic sequences when working with shotgun sequence data.
2. higher resolution for all eukaryotic sequences using mostly un-curated annotations from NCBI Taxonomy, when higher level taxonomy agreed with SILVA's and when SILVA's taxonomy did not go to higher resolution.

LCAClassifier v3.0.7

Minor release with bugfix for amoA database.

The LCAClassifier now supports the use of an additional reference database, for phylogenetic classification of the archaeal ammonia monooxygenase (amoA) gene, developed by Alves et al.

LCAClassifier v3.0.6

The LCAClassifier now supports the use of an additional reference database, for phylogenetic classification of the archaeal ammonia monooxygenase (amoA) gene, developed by Alves et al.

LCAClassifier v3.0.5

LCAClassifierV3.0.5.tar.gz
Fixed installation issue due to zc.buildout update

LCAClassifier v3.0.4

Support for new UNITE reference database (v7.2) and minor bugfixes of silvamod128 taxonomy and nds2CREST parsing of SILVA-type numeric taxa (e.g. "Proteobacteria_2"), which are merged but previously failed to conserve species names.

LCAClassifier v3.0.3

Fixes installation issues in some Linux distributions by forcing older version of BIOM-format (and thus Numpy).

LCAClassifier v3.0.2

Major release featuring a compete source code overhaul, faster classification (thanks to smaller .tre files), support for taxon-specific minimum percentage identity, faster and easier construction of custom reference databases and strict rank enforcement. The default reference database for SSU rRNA is now SilvaMod v128 (based on SILVA v128).