LICENSE.md
MANIFEST.in
README.md
setup.py
docs/.gitignore
docs/Makefile
docs/annotate.rst
docs/commands.rst
docs/compare.rst
docs/conda.rst
docs/conf.py
docs/databases.rst
docs/dependencies.rst
docs/docker.rst
docs/evidence.rst
docs/index.rst
docs/install.rst
docs/make.bat
docs/manual.rst
docs/predict.rst
docs/prepare.rst
docs/tutorials.rst
docs/update.rst
docs/utilities.rst
funannotate/__init__.py
funannotate/__version__.py
funannotate/annotate.py
funannotate/check.py
funannotate/clean.py
funannotate/compare.py
funannotate/database.py
funannotate/downloads.json
funannotate/fix.py
funannotate/interlap.py
funannotate/iprscan.py
funannotate/library.py
funannotate/mask.py
funannotate/outgroups.py
funannotate/predict.py
funannotate/remote.py
funannotate/resources.py
funannotate/setupDB.py
funannotate/sort.py
funannotate/species.py
funannotate/stackedBarGraph.py
funannotate/test.py
funannotate/train.py
funannotate/update.py
funannotate.egg-info/PKG-INFO
funannotate.egg-info/SOURCES.txt
funannotate.egg-info/dependency_links.txt
funannotate.egg-info/requires.txt
funannotate.egg-info/top_level.txt
funannotate/aux_scripts/augustus_parallel.py
funannotate/aux_scripts/enrichment_parallel.py
funannotate/aux_scripts/fasta2agp.pl
funannotate/aux_scripts/filterGenemark.pl
funannotate/aux_scripts/filterIntronsFindStrand.pl
funannotate/aux_scripts/funannotate-BUSCO2-py2.py
funannotate/aux_scripts/funannotate-BUSCO2.py
funannotate/aux_scripts/funannotate-p2g.py
funannotate/aux_scripts/funannotate-runEVM.py
funannotate/aux_scripts/genemark_gtf2gff3.pl
funannotate/aux_scripts/getEggNog.sh
funannotate/aux_scripts/hmmer_parallel.py
funannotate/aux_scripts/iprscan-local.py
funannotate/aux_scripts/iprscan2annotations.py
funannotate/aux_scripts/pal2nal.pl
funannotate/aux_scripts/phobius-multiproc.py
funannotate/aux_scripts/phobius-remote.pl
funannotate/aux_scripts/runIPRscan.py
funannotate/aux_scripts/sam2bam.sh
funannotate/aux_scripts/tbl2asn_parallel.py
funannotate/aux_scripts/trinity.py
funannotate/aux_scripts/trnascan2gff3.pl
funannotate/aux_scripts/xmlcombine.py
funannotate/config/EOG092C0B3U.prfl
funannotate/config/TruSeq3-PE.fa
funannotate/config/TruSeq3-SE.fa
funannotate/config/busco_test.fa
funannotate/config/codeml.config
funannotate/config/extrinsic.E.XNT.RM.cfg
funannotate/config/smcogs.txt
funannotate/config/test.sbt
funannotate/config/tf_interpro.txt
funannotate/html_template/css/bootstrap.min.css
funannotate/html_template/css/starter-template.css
funannotate/html_template/js/bootstrap.min.js
funannotate/html_template/js/ie-emulation-modes-warning.js
funannotate/html_template/js/ie10-viewport-bug-workaround.js
funannotate/html_template/js/jquery.min.js
funannotate/utilities/__init__.py
funannotate/utilities/bam2gff3.py
funannotate/utilities/contrast.py
funannotate/utilities/gbk2parts.py
funannotate/utilities/gff2prot.py
funannotate/utilities/gff2tbl.py
funannotate/utilities/quarry2gff3.py
funannotate/utilities/stats.py
funannotate/utilities/stringtie2gff3.py
funannotate/utilities/tbl2gbk.py
scripts/funannotate