Gtdbtk

* Best translation table displayed in summary file.
* GTDB-Tk now supports gzipped genomes as inputs (--extension .gz).
* By default, GTDB-Tk uses precalculated RED values.
* New option to recalculate RED value during classify step (--recalculate_red).
* New option to export the untrimmed reference MSA files.
* New option to skip_trimming during align step.
* New option to use a custom taxonomy file when rooting a tree.
* New [FAQ](https://github.com/Ecogenomics/GTDBTk/blob/stable/docs/faq.md) page available.
* New output structure.
* This version requires a new version of the GTDB-Tk data package (gtdbtk_r89_data.tar.gz) available [here](https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/)

- Fix scratch_dir (--mmap-file) option.

* Species classification is now based strictly on the ANI to reference genomes
* The "classify" function now reports the closest reference genome in the summary file even if the ANI is <95%
* The summary.tsv file has 4 new columns: aa_percent, red_values, fastani_reference_radius, and warnings
* By default, the "align" function now performs the same MSA trimming used by the GTDB
* New pplacer support for writing to a scratch file (--mmap-file option)
* Random seed option for MSA trimming has been added to allow for reproducible results
* Configuration of the data directory is now set using the environmental variable GTDBTK_DATA_PATH (see [pip installation](pip-installation))
* Perl dependencies has been removed
* Python libraries biolib, mpld3 and jinja have been removed
* This version requires a new version of the GTDB-Tk data package (gtdbtk.r86_v2_data.tar.gz) available [here](https://data.ace.uq.edu.au/public/gtdbtk/release_86/)

- align step in classify_wf and de_novo_wf function has been fixed.
- improve summary file output.
- "align" function now supports the same custom trimming GTDB will be performing.
- returns closest reference genome to summary file (even if the ANI is less than 95%)
- bug fixing

- v0.1.3 resolves bug that would occur when a user genome has a FastANI >= 95% with reference genomes but not with the closest pplacer leaf node.

Release 0.1.2 addresses a bug that would occasionally cause genomes to not be correctly associated with a reference genome in the pplacer tree. FastANI was still identifying correct species assignments.