.gitignore
.zenodo.json
CITATION.cff
CONTRIBUTING.md
Dockerfile
LICENSE
MANIFEST.in
NOTICE
README.md
README_CN.md
README_EN.md
codemeta.json
environment.yml
pyproject.toml
requirements.txt
_figtree_patch/BUILD_PROVENANCE.md
_figtree_patch/README.md
_figtree_patch/figtree_original.jar
_figtree_patch/src/figtree/treeviewer/decorators/AttributableDecorator.java
_figtree_patch/src/figtree/treeviewer/decorators/DiscreteColourDecorator.java
_figtree_patch/src/figtree/treeviewer/painters/ScaleAxisPainter.java
_figtree_patch/src/figtree/treeviewer/treelayouts/RadialTreeLayout.java
benchmarks/benchmark_meta.json
benchmarks/competitive_results.csv
benchmarks/figure2_main.pdf
benchmarks/figure2_main.png
benchmarks/figure_s1.pdf
benchmarks/figure_s1.png
benchmarks/figure_s2.pdf
benchmarks/figure_s2.png
benchmarks/figure_s5.pdf
benchmarks/figure_s5.png
benchmarks/figure_s6.pdf
benchmarks/figure_s6.png
benchmarks/figure_s7.pdf
benchmarks/figure_s7.png
benchmarks/full_benchmark.py
benchmarks/gtdb_benchmark.py
benchmarks/gtdb_results.json
benchmarks/make_figures.py
benchmarks/performance.py
benchmarks/results.csv
benchmarks/results_annotations.csv
benchmarks/results_shapes.csv
benchmarks/slope_summary.json
benchmarks/stage_breakdown.csv
benchmarks_frozen_backup_2026-08-26/benchmark_meta.json
benchmarks_frozen_backup_2026-08-26/competitive_results.csv
benchmarks_frozen_backup_2026-08-26/figure2_main.pdf
benchmarks_frozen_backup_2026-08-26/figure2_main.png
benchmarks_frozen_backup_2026-08-26/figure_s1.pdf
benchmarks_frozen_backup_2026-08-26/figure_s1.png
benchmarks_frozen_backup_2026-08-26/figure_s2.pdf
benchmarks_frozen_backup_2026-08-26/figure_s2.png
benchmarks_frozen_backup_2026-08-26/figure_s5.pdf
benchmarks_frozen_backup_2026-08-26/figure_s5.png
benchmarks_frozen_backup_2026-08-26/figure_s6.pdf
benchmarks_frozen_backup_2026-08-26/figure_s6.png
benchmarks_frozen_backup_2026-08-26/figure_s7.pdf
benchmarks_frozen_backup_2026-08-26/figure_s7.png
benchmarks_frozen_backup_2026-08-26/full_benchmark.py
benchmarks_frozen_backup_2026-08-26/gtdb_benchmark.py
benchmarks_frozen_backup_2026-08-26/gtdb_results.json
benchmarks_frozen_backup_2026-08-26/make_figures.py
benchmarks_frozen_backup_2026-08-26/performance.py
benchmarks_frozen_backup_2026-08-26/results.csv
benchmarks_frozen_backup_2026-08-26/results_annotations.csv
benchmarks_frozen_backup_2026-08-26/results_shapes.csv
benchmarks_frozen_backup_2026-08-26/slope_summary.json
benchmarks_frozen_backup_2026-08-26/stage_breakdown.csv
docs/comparison_CN.md
docs/comparison_EN.md
docs/user_manual_CN.md
docs/user_manual_EN.md
examples/01_basic_usage.py
examples/02_visual_test.py
examples/03_render_with_figtree.py
examples/04_generate_test_results.py
examples/05_gtdb_workflow.py
examples/06_beast_laca_workflow.py
examples/benchmarks/generate_datasets.py
examples/benchmarks/hiv_env.tre
examples/benchmarks/mammalian_mitogenome.tre
examples/benchmarks/rrna_16s.tre
examples/data/FigTree_withLACA_CLK_95CI.tree.recover
examples/data/FigTree_withLACA_CLK_95CI.tsv
examples/data/README.md
figtreekit/__init__.py
figtreekit/__main__.py
figtreekit/_cli.py
figtreekit/_defaults.py
figtreekit/_figtree_setup.py
figtreekit/_parser.py
figtreekit/_renderer.py
figtreekit/_serializer.py
figtreekit/_version.py
figtreekit/annotations.py
figtreekit/enums.py
figtreekit/exceptions.py
figtreekit/figtree_patched.jar
figtreekit/py.typed
figtreekit/styler.py
figtreekit/taxonomy.py
figtreekit/validators.py
figtreekit.egg-info/PKG-INFO
figtreekit.egg-info/SOURCES.txt
figtreekit.egg-info/dependency_links.txt
figtreekit.egg-info/entry_points.txt
figtreekit.egg-info/requires.txt
figtreekit.egg-info/scm_file_list.json
figtreekit.egg-info/scm_version.json
figtreekit.egg-info/top_level.txt
notebooks/01_basic_styling.ipynb
notebooks/02_clade_highlighting.ipynb
notebooks/03_beast_output.ipynb