Cenote-Taker 2 Version 2.1.1

If you haven't already installed Cenote-Taker 2, please follow installation instructions in README. If you have already installed it, please do: cd Cenote-Taker2 then git pull. Then update the HMM database.
Thank you.

The code was largely re-written to increase parallelization, making runs with any number of contigs of any length run much faster. I've improved the output file structure to make a more sensible summary (.tsv) file, and I've put all the genome maps (.gbf) and gene tables (.gtf) in a single directory (sequin_and_genome_maps/). I've added some additional options to make the user experience more intuitive, especially the -am True option which makes Cenote-Taker 2 assume that all input sequences are viral, and will simply annotate them. On the other hand, I've written code for Cenote Unlimited Breadsticks (unlimited_breadsticks.py) and included it in the Cenote-Taker 2 repo. The Unlimited Breadsticks tool is ONLY the discovery and pruning modules of Cenote-Taker 2. It runs dramatically faster than Cenote-Taker 2, as it skips all annotation steps. I still urge users to generate and examine genome maps for important virus sequences in order to manually inspect putative viruses.
Finally, I've removed about 100 HMMs from the hallmark gene database, and added about 50 new HMMs. The removed HMMs, while generated from virus sequences, were also found in non-virus regions of bacterial chromosomes, making them unsuitable for virus discovery.
Best of luck :)
Mike