├── .gitattributes ├── .gitignore ├── .pre-commit-config.yaml ├── .zenodo.json ├── AAFTF ├── AAFTF_main.py ├── __init__.py ├── __version__.py ├── assemble.py ├── assess.py ├── data │ ├── mito-seed.fasta │ └── novoplasty-config.txt ├── fcs_gx_purge.py ├── fcs_screen.py ├── filter.py ├── fix_tbl.py ├── mito.py ├── pipeline.py ├── polish.py ├── resources.py ├── rmdup.py ├── sort.py ├── sourpurge.py ├── trim.py ├── utility.py ├── vecscreen.py └── version_hardcode.py ├── CHANGES.md ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASE_NOTES.md ├── TODO.md ├── ci └── recipe │ └── meta.yaml ├── docs ├── AAFTF.png ├── AAFTF_card.png ├── Makefile ├── conf.py └── index.rst ├── environment.yml ├── patches ├── polca.patch └── polca.sh ├── pyproject.toml ├── requirements.txt ├── scripts ├── AAFTF └── __init__.py ├── setup.cfg ├── setup.py └── tests ├── 00_dipspades.sh ├── 00_megahit.sh ├── 00_spades_1trim.sh ├── 00_spades_2trim.sh ├── 00_spades_2trim_fastp1st.sh ├── 00_spades_2trim_fastp1st_isolate.sh ├── 00_spades_3trim.sh ├── 00_spades_fastptrim.sh ├── 00_spades_nomerge.sh ├── 01_mito.sh ├── 03_BUSCO.sh ├── 04_make_summary.sh ├── __init__.py ├── asm_stats.pl ├── asm_stats.tsv └── augustus_config ├── cgp ├── log_reg_parameters_arabidopsis.cfg ├── log_reg_parameters_default.cfg ├── log_reg_parameters_fly.cfg ├── log_reg_parameters_human.cfg ├── log_reg_parameters_primates.cfg └── log_reg_parameters_s_aureus.cfg ├── extrinsic ├── extrinsic-cgp.cfg ├── extrinsic.E.XNT.cfg ├── extrinsic.E.cfg ├── extrinsic.M.RM.E.W.cfg ├── extrinsic.M.RM.PB.cfg ├── extrinsic.ME.cfg ├── extrinsic.MEMS.cfg ├── extrinsic.MP.cfg ├── extrinsic.MPE.cfg ├── extrinsic.MT.cfg └── extrinsic.cfg ├── model ├── constraints_shadow_partial.txt ├── constraints_shadow_partial_utr.txt ├── ovlp_len.pbl ├── ovlp_len_archaea.pbl ├── states_shadow.cfg ├── states_shadow_2igenic.cfg ├── states_shadow_bacterium.cfg ├── states_shadow_intronless.cfg ├── states_shadow_utr.cfg ├── states_shadow_utr_nc.cfg ├── states_singlestrand.cfg ├── states_singlestrand_2igenic.cfg ├── trans_shadow_atleastone.pbl ├── trans_shadow_bacterium.pbl ├── trans_shadow_complete.pbl ├── trans_shadow_complete_utr.pbl ├── trans_shadow_exactlyone.pbl ├── trans_shadow_intronless.pbl ├── trans_shadow_partial.pbl ├── trans_shadow_partial_utr.pbl ├── trans_shadow_partial_utr_nc.pbl ├── trans_singlestrand_atleastone.pbl ├── trans_singlestrand_complete.pbl ├── trans_singlestrand_exactlyone.pbl └── trans_singlestrand_partial.pbl ├── profile ├── blosum55.qij ├── blosum62.qij └── default.qij └── species ├── anidulans ├── anidulans_exon_probs.pbl ├── anidulans_igenic_probs.pbl ├── anidulans_intron_probs.pbl ├── anidulans_parameters.cfg └── anidulans_weightmatrix.txt └── generic ├── generic_metapars.cfg ├── generic_metapars.cgp.cfg ├── generic_metapars.utr.cfg ├── generic_parameters.cfg └── generic_weightmatrix.txt /.gitattributes: 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