GToTree v1.8.10

• saving ncbi downloaded files when debug flag (-d) is set as requested in #95, implemented in #102
  • with the debug flag set while running, it will keep specific files in <output_dir>/<tmp_dir>/ncbi-downloads/:
    • if amino-acid seqs are used, it will keep the downloaded amino-acid seqs
    • if there were no amino-acid seqs, and the genome had to be downloaded, it will keep the downloaded genome and the prodigal-called amino-acid seqs
    • if using nucleotide mode (-z), it will keep the downloaded genome and the prodigal-called nt cds and amino-acid seqs

GToTree v1.8.9

• added logic to catch, exit, and report when muscle doesn't successfully produce an alignment for a single-copy gene-set (thanks to #101)

GToTree v1.8.8

• properly saving additional pfam target HMMs when that functionality is used
• updated the call to FastTree and FastTreeMP to be include -nt and -gtr when GToTree is run in nucleotide mode (-z)

GToTree v1.8.7

• improvements to the "Universal" Hug et al. gene set thanks so much to @molly-kholodova digging in and reaching out!

  • PF00181 ("Ribosomal_L2") was changed to PF03947 ("Ribosomal_L2_C")
    • the C-terminal (which PF03947 covers) is better conserved
  • PF00827 ("Ribosomal_L15") was changed to PF00828 ("Ribosomal_L27A")
    • PF00827 was archaea/euk only, PF00828 holds the bac/arc L15 also
  • PF17135 ("Ribosomal_L18") was changed to PF00861 ("Ribosomal_L18p")
    • the PF00861 model is better distributed

• gtt-gen-SCG-HMMs now reports which version of PFAM was used (prints it out to the terminal and writes it to a file)

Full Changelog: v1.8.6...v1.8.7

GToTree v1.8.6

• fixed when taxonomy information wasn't being added to labels when running in nucleotide mode (-z; #91)

GToTree v1.8.5

• update to gtt-gen-SCG-HMMs to deal with ncbi assembly summary files having a column name of "#assembly_accession" instead of what was once "# assembly_accession"

GToTree v1.8.4

• fixed an issue that prevented moving forward when there were more than 12,500 input genomes (#83)
  • when there are greater than 12,500 input genomes, there is a notice to the user and it requires action to continue or cancel the run
  • before somehow i left that always exiting no matter what, this fix addresses that and lets folks continue

GToTree v1.8.3

• updated links to GTDB files as they switched from .tar.gz extensions to .tsv.gz extensions in latest release, thanks to note from @jmtsuji (#81)

GToTree v1.8.2

• added http option to gtt-test.sh (gtt-test.sh http) thanks to #78 (8035115)
• updated gtt-get-ncbi-tax-data to appropriately pull from http instead of ftp also thanks to #78
• fix to check for ncbi assemblies "date-retrieved.txt" file, as also caught and fixed by @hyphaltip (#80) 🙏 (9eb248a)

v1.8.1

• removing update to gnu-getopt done in https://github.com/AstrobioMike/GToTree/releases/tag/v1.8.0
  • it's not available via conda for linux, and even though it's native, i can't remove the requirement just from mac conda installs (where it isn't native) :(