2023-10-03.build7061

This release is based on PGAP-6.6. It includes the following features and bug fixes:

• Lowered pseudogene false positive rate by improving protein alignment handling during structural annotation
• Designed new hidden Markov models (HMMs) for validated small proteins, for improving structural annotation
• Adopted PFAM release 35, for help in structural and functional annotation
• Bug fixes:
  • Podman container name is now respected, #270
  • Empty undocumented files now deleted from output
  • Removed extra # in annot_with_genomic_fasta.gff
• pgap.py -g option now supports absolute paths
• If output directory exists, exit rather than add a suffix

Third Party Software and Data versions used:

• GeneOntology 2023-07-27
• tRNAscan-SE 2.0.12
• hmmer v.3.1b2
• CRISPR v.1.02
• AntiFam v.3.0
• Rfam v.14.4
• GeneMarkS-2 v.1.14_1.25
• infernal v.1.1.4