A Coded Phenotypic Character Matrix Generator, version 1.0 (released Feb 23, 2017).

MicroPIEDigester is a perl script that converts raw phenotypic character information generated by MicroPIE (Microbial Phenomic Information Extractor; https://github.com/biosemantics/micropie2). The Digester codes the raw phenotypic information into characters and character states, extracting both discrete and continuous character types, and outputs nexus files formatted for Mesquite (http:https://mesquiteproject.org/). In the process of character coding, it uses the standard vocabulary and synonyms of terms established in MicrO (An Ontology of Prokaryotic Phenotypic and Metabolic Characters; https://github.com/carrineblank/MicrO/) to ontologize raw phenotypic characters into character states.

Created in September through October of 2016 by Carrine E. Blank, University of Montana.

Citation: Blank CE, Moore LR, Thacker RW, Cui H, Mao J. 2017. A semi-automated pipeline for the large-scale analysis of phenotypic character evolution in prokaryotic taxa; emerging patterns of niche evolution using Bacteroidetes as a test case. In prep.

MicroPIEDigester is invoked at the command line by typing 'perl MicroPIEDigester.pl infile' where the infile is a character matrix in text format.

MicroPIEDigester version 1.0 was created to code character information for the Bacteroidetes. Processes the following characters types: median mol %g+c, cell shape, mean cell length, max cell length, mean cell width, max cell width, cell relationships&aggregations, gram stain type, internal features, motility, pigment compounds, NaCl minimum, NaCl optimum, NaCl maximum, pH minimum, pH optimum, pH maximum, temperature minimum, temperature optimum, temperature maximum, aerophilicity, magnesium requirement for growth, vitamins and cofactors required for growth, antibiotic sensitivity, antibiotic resistant, colony shape, colony margin, colony texture, and colony color.