TransDecoder Release v5.2.0

@brianjohnhaas brianjohnhaas released this Apr 21, 2018 · 16 commits to master since this release

Allow to rerun w/ blast and pfam results and to just reexecute the steps needed to take those data into account.
The test runner now includes a small pfam and blast on-the-fly execution step as well.

TransDecoder Release v5.1.0

@brianjohnhaas brianjohnhaas released this Mar 27, 2018 · 34 commits to master since this release

Better support for different genetic codes as described here:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Also, shouldn't report UTR records for cases where the coding region starts at a partial codon.

TransDecoder-v5.0.2 Release

@brianjohnhaas brianjohnhaas released this Oct 20, 2017 · 41 commits to master since this release

-protein identifiers are more manageable (ex. ${transcript_acc}.p1, .p2, ..., .pn)
-added example for use w/ supertranscripts

TransDecoder Release v5.0.1

@brianjohnhaas brianjohnhaas released this Sep 12, 2017 · 50 commits to master since this release

the start-adjustment can now cope with sequences containing non-{GATC} characters.

TransDecoder Release v5.0.0

@brianjohnhaas brianjohnhaas released this Aug 26, 2017 · 54 commits to master since this release

-algorithm updates: frame[0] score > 0 and max for first 3 reading frames (instead of all 6), and orf with highest frame[0] score is chosen allowing for minimal overlap among selected predictions.
-option --single_best_only provides the single longest of the selected orfs per contig.
-long orfs unlikely to appear in random sequence are automatically selected as candidates with this minimal long orf length set dynamically according to GC content.
-orf score and blast or pfam info is propagated to gff3 output

TransDecoder Release v4.1.0

@brianjohnhaas brianjohnhaas released this Aug 17, 2017 · 72 commits to master since this release

-single best orf now selected by default. If more than the single best orf is wanted, use the --all_good_orfs parameter.
-start codon refinement is now done by default. To turn it off and get the original behavior of extending to the longest orf position, use parameter: --no_refine_starts
-cdhit has been removed and replaced by our own fast method for removing redundancies.
-selection of coding regions is strictly governed by Markov-based likelihood scores across reading frames. No auto-retention of long orfs by default, but can be activated by parameter: --retain_long_orfs_length
-rigorously tested and benchmarked for prediction accuracy