├── .gitmodules ├── README.rst ├── blast_nearby └── blast_nearby.py ├── gap_simulations ├── fractionation_ga.py ├── likelihood_ratio_test.py ├── plot_sims.py ├── run.sh └── sims │ ├── runs.a.deletions.actual.1.A.txt │ ├── runs.a.deletions.actual.1.B.txt │ ├── runs.a.deletions.sim.1.A.txt │ ├── runs.a.deletions.sim.1.B.txt │ ├── runs.a.deletions.sim.2.A.txt │ ├── runs.a.deletions.sim.2.B.txt │ ├── runs.a.deletions.sim.3.A.txt │ ├── runs.a.deletions.sim.3.B.txt │ ├── runs.b.deletions.actual.1.A.txt │ ├── runs.b.deletions.actual.1.B.txt │ ├── runs.b.deletions.sim.1.A.txt │ ├── runs.b.deletions.sim.1.B.txt │ ├── runs.b.deletions.sim.2.A.txt │ ├── runs.b.deletions.sim.2.B.txt │ ├── runs.b.deletions.sim.3.A.txt │ ├── runs.b.deletions.sim.3.B.txt │ ├── runs.c.deletions.actual.1.A.txt │ ├── runs.c.deletions.actual.1.B.txt │ ├── runs.c.deletions.sim.1.A.txt │ ├── runs.c.deletions.sim.1.B.txt │ ├── runs.c.deletions.sim.2.A.txt │ ├── runs.c.deletions.sim.2.B.txt │ ├── runs.c.deletions.sim.3.A.txt │ └── runs.c.deletions.sim.3.B.txt ├── gbs_digest ├── cmdline.c ├── cmdline.h ├── gbs_digest.c ├── gbs_digest.ggo ├── kseq.h ├── makefile └── test.fq.gz ├── gff_loader ├── README.rst ├── gff_loader.py └── run.sh ├── klib ├── README.rst ├── nim │ ├── htlib.nim │ ├── htlib.nimble │ ├── klib │ ├── kseq.h │ └── test.fasta.gz ├── setup.py ├── src │ ├── __init__.py │ ├── kopen.pxd │ ├── kopen.pyx │ ├── kseq.h │ ├── kseq.pxd │ ├── kseq.pyx │ └── zlib.pxd └── tests │ ├── data │ └── test.fasta │ └── test_kseq.py ├── last_wrapper ├── README.rst ├── last.py ├── last_helper.py ├── lastal ├── lastdb ├── lastex └── patch ├── lastz_wrapper └── blastz.py ├── notebooks ├── kmer │ ├── Assembly-kmer-estimates.ipynb │ ├── reads.histo │ └── run.sh ├── patent-scraper │ └── Google-patent-scraper.ipynb └── segment-anything │ └── Segment Anything.ipynb ├── phasing ├── README.rst ├── main.cc ├── main.h ├── makefile └── program.cc ├── poaV2 ├── LICENSE ├── Makefile ├── README.rst ├── align_lpo.c ├── align_lpo2.c ├── align_lpo_po.c ├── align_lpo_po2.c ├── align_score.c ├── align_score.h ├── black_flag.c ├── black_flag.h ├── blosum80.mat ├── blosum80_trunc.mat ├── buildup_lpo.c ├── create_seq.c ├── default.h ├── fasta_format.c ├── heaviest_bundle.c ├── lpo.c ├── lpo.h ├── lpo_format.c ├── main.c ├── make_pscores.pl ├── msa_format.c ├── msa_format.h ├── multidom.pscore ├── multidom.seq ├── numeric_data.c ├── poa.h ├── project.h ├── remove_bundle.c ├── seq_util.c ├── seq_util.h └── stringptr.c ├── pybiomart ├── README.rst ├── biomart │ ├── __init__.py │ └── __init__.pyc ├── scripts │ └── phytozome_to_bed.py └── setup.py ├── synonymous_calculation ├── README.pdf ├── README.rst ├── bin │ ├── clustalw2 │ └── yn00 ├── data │ ├── test.cds │ ├── test.ks │ └── test.pep ├── report_ks.py ├── run.sh └── synonymous_calc.py ├── synteny-pipeline ├── README.rst ├── maftools │ ├── README.rst │ ├── maf_chains.py │ ├── maf_select.py │ ├── maf_to_bed.py │ └── maf_to_blast8.py └── synteny_graph │ ├── README.rst │ 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