GToTree v1.8.16

• Fix to gtt-get-accessions-from-GTDB erroring out after initial use thanks to note from @MariaAVC

GToTree v1.8.15

Added

• added a flag to gtt-get-accessions-from-GTDB (--use-ecogenomics) to allow specifing to download from data.gtdb.ecogenomic.org/releases instead of the default data.ace.uq.edu.au/public/gtdb/data/releases thanks to the suggestion from @Stian-2rz (#107)
• a partitions file in nexus format (<outdir>/run_files/Partitions.nex) is produced in addition to the regular text-formatted one (<outdir>/run_files/Partitions.txt), because for some iqtree model settings the txt format has leads to a bug – also thanks to @Stian-2rz! (#108)

Changed

• currently skipping certificate checking on GTDB downloads (prompted from #107)
  • this impacts gtt-get-accessions-from-GTDB and the internally used gtt-check-or-setup-GTDB-files

GToTree v1.8.14

• change to taxonkit call when adding NCBI tax info (now using reformat2 and a pattern) in order to deal with NCBI tax-structure update

GToTree v1.8.13

• change to gtt-gen-SCG-HMMs to only use Pfam 37.0 for now (as later versions don't have one of the required files; see #104)

GToTree v1.8.12

• changed GTDB download links from https://data.gtdb.ecogenomic.org/releases/ to https://data.ace.uq.edu.au/public/gtdb/data/releases/ due to the former becoming prohibitively slow recently

GToTree v1.8.11

• added VeryFastTree as a treeing method option thanks to user-feedback from @jianshu93 (#96; 6d997f9)

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