GToTree v1.5.51

• updating gtt-gen-SCG-HMMs as the pfam info column holding 'average coverage of sequence by domain' changed

GToTree v1.5.50

• adding version info to workflow-specific citations.txt file produced with run

GToTree v1.5.48

• adding FastTreeMP usage by default if on linux, thanks to note/suggestion from @hyphaltip here: #33

GToTree v1.5.47

• adding L15 to Universal Hug set as per kind note here: #30

GToTree v1.5.46

• Cancelling the run immediately and notifying user if -L desired lineage information was provided, but neither -t nor -D flags were set telling GToTree which taxonomy to use. Previously it would just run and not modify the headers of the output alignment or tree files.

GToTree v1.5.45

• finishes fixing the empty final column issue in the SCG_hit_counts.tsv file

GToTree v1.5.44

• removes extra blank column that was being added to SCG_hit_counts.tsv file

GToTree v1.5.43

• adding helper script to remove all-gap seqs from alignment, gtt-remove-all-gap-seqs-from-alignment

GToTree v1.5.42

• bug fix
  • since addition of gtt-cat-alignments in 1.5.30, needed to adjust how the Partitions.txt file was generated due to different ordering sometimes occurring between how python would glob the alignment files vs how bash ls sorted them
• added -k option to retain individual protein alignments if wanted

GToTree v1.5.41

• adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing to new documentation