mycotools 0.9b1

A compilation of bioinformatic and computation biology inspired python tools

PURPOSE

MycoTools is a compilation of computational biology tools and database (MycoDB) software designed to increase throughput analyzing fungal genomic data (JGI & NCBI). MycoDB is a database schema with uniform gene coordinate (gff) and fasta header curation, systematic code naming, and modularity as guiding principles, which enable analyses with datasets of 1000s of fungi to as few as 1 or 2. MycoDB is not available outside of the Ohio Supercomputer Center until we publish the tools. Please email [e-mail] if you are interested in becoming an early adopter.

By integrating with the curated MycoDB, MycoTools cuts time on routine tasks like retrieving gff or fasta accessions, running and compiling fastas of MycoDB BLAST/hmmsearches, and other analyses like creating a phylogeny with fa2tree.py or wrangling your dataset with agglomerative clustering via aggClus.py. MycoTools includes sets of utilities that also enable easy acquisition of batches of sequence data using ncbiDwnld.py and jgiDwnld.py.

USAGE

Check out the USAGE.md for a guide on the possibilities MycoTools can enable in your research.

CITING

If MycoTools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the MycoTools version in line.