├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ ├── main.yml │ ├── python-publish.yml │ ├── release-triggered.yml │ ├── release.yml │ ├── singularity-deploy.yml │ └── triggered-build.yml ├── .gitignore ├── .readthedocs.yaml ├── .zenodo.json ├── CITATION.cff ├── Dockerfile ├── Dockerfile2 ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── Singularity ├── docs ├── .gitignore ├── Makefile ├── annotate.rst ├── commands.rst ├── compare.rst ├── conda.rst ├── conf.py ├── databases.rst ├── dependencies.rst ├── docker.rst ├── evidence.rst ├── index.rst ├── install.rst ├── make.bat ├── manual.rst ├── predict.rst ├── prepare.rst ├── requirements.txt ├── tutorials.rst ├── update.rst └── utilities.rst ├── funannotate-docker ├── funannotate-logo.png ├── funannotate-podman ├── funannotate ├── __init__.py ├── __version__.py ├── annotate.py ├── aux_scripts │ ├── augustus_parallel.py │ ├── enrichment_parallel.py │ ├── fasta2agp.py │ ├── filterGenemark.pl │ ├── filterIntronsFindStrand.pl │ ├── funannotate-BUSCO2-py2.py │ ├── funannotate-BUSCO2.py │ ├── funannotate-p2g.py │ ├── funannotate-runEVM.py │ ├── genemark_gtf2gff3.pl │ ├── getEggNog.sh │ ├── hmmer_parallel.py │ ├── iprscan-local.py │ ├── iprscan2annotations.py │ ├── pal2nal.pl │ ├── phobius-multiproc.py │ ├── phobius-remote.pl │ ├── runIPRscan.py │ ├── sam2bam.sh │ ├── tbl2asn_parallel.py │ ├── trinity.py │ ├── trnascan2gff3.pl │ └── xmlcombine.py ├── check.py ├── clean.py ├── compare.py ├── config │ ├── EOG092C0B3U.prfl │ ├── TruSeq3-PE.fa │ ├── TruSeq3-SE.fa │ ├── busco_test.fa │ ├── codeml.config │ ├── extrinsic.E.XNT.RM.cfg │ ├── smcogs.txt │ ├── test.sbt │ └── tf_interpro.txt ├── database.py ├── downloads.json ├── fix.py ├── funannotate.py ├── html_template │ ├── css │ │ ├── bootstrap.min.css │ │ └── starter-template.css │ └── js │ │ ├── bootstrap.min.js │ │ ├── ie-emulation-modes-warning.js │ │ ├── ie10-viewport-bug-workaround.js │ │ └── jquery.min.js ├── interlap.py ├── iprscan.py ├── library.py ├── 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