• compatible with hmmsearch or hmmscan output
• cleaner organization of outputs and checkpoints
• TransDecoder.LongOrfs includes option for --complete_orfs_only (as requested)
• GFF3 files no longer have the uri-encoding so easier to directly read.
• misc bugfixes - corrected length in fasta header for start-refined orfs

(and earlier updates from 5.6.0 that apparently never officially released)

• genome propagation of orfs resets orientation for unspliced transcripts with opposite strand orfs.
• speed update from Yanick Paco Hagemeijer
• added option --output_dir | -O to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basename(target.fasta) + ".transdecoder_dir/").
• removing track name from bed output
• if select single best orf, do selection before removing overlapping preds
• updated get_longest_ORF_per_transcript.pl to match current header formatting
• really retain all blast hits, ignoring overlaps to prev selected entries, unless single_best_orf indicated
• updated genetic code options in help menu