python-scripts/clade.smk
python-scripts/interactive_tree.R
python-scripts/msa.smk
python-scripts/phylo.smk
python-scripts/reconstruction.smk
site-packages/squirrel-1.1.6.dist-info/INSTALLER
site-packages/squirrel-1.1.6.dist-info/METADATA
site-packages/squirrel-1.1.6.dist-info/RECORD
site-packages/squirrel-1.1.6.dist-info/REQUESTED
site-packages/squirrel-1.1.6.dist-info/WHEEL
site-packages/squirrel-1.1.6.dist-info/direct_url.json
site-packages/squirrel-1.1.6.dist-info/entry_points.txt
site-packages/squirrel-1.1.6.dist-info/licenses/LICENSE
site-packages/squirrel-1.1.6.dist-info/top_level.txt
site-packages/squirrel/__init__.py
site-packages/squirrel/command.py
site-packages/squirrel/data/NC_001611.fasta
site-packages/squirrel/data/NC_003310.fasta
site-packages/squirrel/data/NC_063383.fasta
site-packages/squirrel/data/background.fasta
site-packages/squirrel/data/background.panel.fasta
site-packages/squirrel/data/background_sample.csv
site-packages/squirrel/data/gene_boundaries.NC_001611.csv
site-packages/squirrel/data/gene_boundaries.cladei.csv
site-packages/squirrel/data/gene_boundaries.cladeii.csv
site-packages/squirrel/data/grantham_score.txt
site-packages/squirrel/data/outgroups.fasta
site-packages/squirrel/data/ref_seq.fasta
site-packages/squirrel/data/report.mako
site-packages/squirrel/data/to_mask.NC_001611.csv
site-packages/squirrel/data/to_mask.cladei.csv
site-packages/squirrel/data/to_mask.cladeii.csv
site-packages/squirrel/scripts/__init__.py
site-packages/squirrel/scripts/clade.smk
site-packages/squirrel/scripts/interactive_tree.R
site-packages/squirrel/scripts/msa.smk
site-packages/squirrel/scripts/phylo.smk
site-packages/squirrel/scripts/reconstruction.smk
site-packages/squirrel/utils/__init__.py
site-packages/squirrel/utils/clade_assignment.py
site-packages/squirrel/utils/cns_qc.py
site-packages/squirrel/utils/config.py
site-packages/squirrel/utils/custom_logger.py
site-packages/squirrel/utils/initialising.py
site-packages/squirrel/utils/io_parsing.py
site-packages/squirrel/utils/log_colours copy.py
site-packages/squirrel/utils/log_colours.py
site-packages/squirrel/utils/log_handler_handle copy.py
site-packages/squirrel/utils/log_handler_handle.py
site-packages/squirrel/utils/make_report.py
site-packages/squirrel/utils/misc.py
site-packages/squirrel/utils/reconstruction_functions.py
