AstrobioMike/GToTree: GToTree v1.8.0

genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://github.com/AstrobioMike/GToTree/commit/1bb79e721a06f85f95abe2acf0a03b6804c5ef24)

• downloaded upon first use
• checked when used again, if older than 4 weeks, will be updated
• can be force updated with gtt-get-ncbi-assembly-tables --force-update
• gtt-data-locations has been updated to hold a location for this

nucleotide mode added (https://github.com/AstrobioMike/GToTree/commit/dbe4798ed09c71013b11a4e1027396b42420534b)

• following request/chat here (https://github.com/AstrobioMike/GToTree/issues/77)
• can only accept ncbi accessions and genome nucleotide fasta files as inputs
  • no amino acid because we can't confidently reverse-translate them to nucleotide seqs for aligning/treeing
  • no genbank because a lot of gymnastics would need to be done to deal with all potential incoming genbank files, will not consider/worry about this unless it becomes a need for users

IQTREE settings changed (https://github.com/AstrobioMike/GToTree/commit/dbe4798ed09c71013b11a4e1027396b42420534b)

• now set to use model-finder (-m MFP; http://www.iqtree.org/doc/Tutorial#choosing-the-right-substitution-model)
• and set to use ultrafast bootstrap (-B 1000; http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-ultrafast-bootstrap-approximation), so long as there are at least 4 genomes

updated to use gnu-getopt in order to enable long cli arguments too (https://github.com/AstrobioMike/GToTree/commit/33f3f68a89aa7289b551fe79a377d67a95b11d47)

• none of the single-letter ones that were present have changed