1 files changed, 23 insertions, 13 deletions
diff --git a/biology/p5-transdecoder/pkg-plist b/biology/p5-transdecoder/pkg-plist
index d394d7fa2914..8ec718231222 100644
--- a/biology/p5-transdecoder/pkg-plist
+++ b/biology/p5-transdecoder/pkg-plist
@@ -1,22 +1,23 @@
 bin/TransDecoder.LongOrfs
-bin/TransDecoder.LongOrfs.bak
 bin/TransDecoder.Predict
-bin/TransDecoder.Predict.bak
+%%SITE_PERL%%/transdecoder/DelimParser.pm
 %%SITE_PERL%%/transdecoder/Fasta_reader.pm
 %%SITE_PERL%%/transdecoder/Fasta_retriever.pm
-%%SITE_PERL%%/transdecoder/GFF3_utils.pm
+%%SITE_PERL%%/transdecoder/GFF3_utils2.pm
+%%SITE_PERL%%/transdecoder/GTF.pm
+%%SITE_PERL%%/transdecoder/GTF_utils2.pm
 %%SITE_PERL%%/transdecoder/Gene_obj.pm
-%%SITE_PERL%%/transdecoder/Gene_obj_indexer.pm
 %%SITE_PERL%%/transdecoder/Longest_orf.pm
 %%SITE_PERL%%/transdecoder/Nuc_translator.pm
-%%SITE_PERL%%/transdecoder/TiedHash.pm
+%%SITE_PERL%%/transdecoder/Overlap_piler.pm
+%%SITE_PERL%%/transdecoder/PWM.pm
+%%SITE_PERL%%/transdecoder/Pipeliner.pm
+%%SITE_PERL%%/transdecoder/Process_cmd.pm
+%%SITE_PERL%%/transdecoder/overlapping_nucs.ph
 libexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
 libexec/transdecoder/compute_base_probs.pl
-libexec/transdecoder/create_start_PSSM.pl
-libexec/transdecoder/cufflinks_gtf_genome_to_cdna_fasta.pl
-libexec/transdecoder/cufflinks_gtf_to_alignment_gff3.pl
-libexec/transdecoder/cufflinks_gtf_to_bed.pl
-libexec/transdecoder/extract_FL_subset.pl
+libexec/transdecoder/exclude_similar_proteins.pl
+libexec/transdecoder/fasta_prot_checker.pl
 libexec/transdecoder/ffindex_resume.pl
 libexec/transdecoder/gene_list_to_gff.pl
 libexec/transdecoder/get_FL_accs.pl
@@ -24,9 +25,18 @@ libexec/transdecoder/get_longest_ORF_per_transcript.pl
 libexec/transdecoder/get_top_longest_fasta_entries.pl
 libexec/transdecoder/gff3_file_to_bed.pl
 libexec/transdecoder/gff3_file_to_proteins.pl
-libexec/transdecoder/index_gff3_files_by_isoform.pl
+libexec/transdecoder/gff3_gene_to_gtf_format.pl
+libexec/transdecoder/gtf_genome_to_cdna_fasta.pl
+libexec/transdecoder/gtf_to_alignment_gff3.pl
+libexec/transdecoder/gtf_to_bed.pl
 libexec/transdecoder/nr_ORFs_gff3.pl
 libexec/transdecoder/pfam_runner.pl
+libexec/transdecoder/refine_gff3_group_iso_strip_utrs.pl
+libexec/transdecoder/refine_hexamer_scores.pl
 libexec/transdecoder/remove_eclipsed_ORFs.pl
-libexec/transdecoder/score_CDS_liklihood_all_6_frames.pl
-libexec/transdecoder/seq_n_baseprobs_to_logliklihood_vals.pl
+libexec/transdecoder/score_CDS_likelihood_all_6_frames.pl
+libexec/transdecoder/select_best_ORFs_per_transcript.pl
+libexec/transdecoder/seq_n_baseprobs_to_loglikelihood_vals.pl
+libexec/transdecoder/start_codon_refinement.pl
+libexec/transdecoder/train_start_PWM.pl
+libexec/transdecoder/uri_unescape.pl