A Coded Phenotypic Character Matrix Generator, version 1.5 (released Jan 23, 2018).

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://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.

Originally 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.

Version 1.0 (released Feb 23, 2017): 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. Developed using a user-corrected phenotypic matrix of Bacteroidetes.

Version 1.1 (released Jun 20, 2017): MicroPIEDigester was expanded to extract phenotypic characters from a diverse collection of 575 Firmicutes. The phenotypic matrix was not user-corrected, i.e., the matrix was a direct output of MicroPIEWeb version 0.1.0.

Version 1.2 (released Aug 9, 2017): MicroPIEDigester was expanded to extract phenotypic character for the physiological tests.

Version 1.3 (released Sept 7, 2017): MicroPIEDIgester was expanded in several ways: The antibiotic resistance/sensitivity and physiological test positive/negative characters were combined. Pigment compounds category duplication was corrected Added character categories: cell length, cell width, external features, organic compounds used, organic compounds not used, inorganic compounds used, inorganic compounds not used, fermentation substrates used, fermentation substrates not used. Digester was expanded to extract phenotypic characters from a collection of 1500 Firmicutes, matrices were direct output of MicroPIE version 0.2.

Version 1.4 (released Sept 19, 2017): The fermentation substrates used/not used categories were combined into a single nexus file. The organic substrates used/not used categories were combined into a single nexus file. The inorganic substrates used/not used categories were combined into a single nexus file. Organic compounds used and Inorganic compounds used extracted by physiological tests positive were moved to their respective categories. Organic compounds not used and Inorganic compounds not used extracted by physiological tests negative were moved to their respective categories. Output for fermentation substrates used was exported to the organic substrates used category. Output for fermentation substrates not used was exported to the organic substrates not used category.

Version 1.5 (released Jan 23, 2018): Expansion of organic substrates and fermentation substrates was made after processing > 2,000 new taxonomic descriptions of Firmicutes. A module to accept and process output .csv files from the Digital Protologue was created. Addition of input flags made in order to process data generated by MicroPIE versions 1.1 and 2.0.