Formatting enhancements

Unified whitespace usage in scripts. Fixed some minor bugs. Removed some unused code.

ORF prediction

Added a simple wrapper for bbmap/FGS++ to predict short ORFs from metagenome reads

v1.3.3

Fixed bug in phylogeny_builder_whole_genome.sh that prevents running if nucleotide files alone are provided.

Reorganized scripts

Makes mass install a bit easier

v1.3.1

Added new features and stability to download_NCBI_genomes.sh. Improved documentation within script help file.

Added NCBI genome download

Added download_NCBI_genomes.sh and associated test code. First working version.

v1.2.3

Fixed bug in phylogeny_builder_whole_genome.sh that prevented running when only FastA nucleotide files were provided

Bug fixes

Fixes an issue in the genome phylogeny script introduced in v1.2.1. Script would fail if only .fna/.fna.gz or only .faa/.faa.gz input files were provided.

New features for genome phylogeny

Added amino acid or gzipped file input support for whole genome phylogeny.

Code refactoring

Added consistent versioning and refactored code