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iqtree / piqtree Public

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ENH: attached rate and motif parameters to cogent3 tree object#49

Merged

rmcar17 merged 15 commits intoiqtree:mainiqtree/piqtree:mainfrom

YapengLang:mainYapengLang/piqtree2:mainCopy head branch name to clipboard

Sep 27, 2024

Conversation Commits15 (15)Checks Files changed

Merged

ENH: attached rate and motif parameters to cogent3 tree object#49
rmcar17 merged 15 commits intoiqtree:mainfrom
YapengLang:main

Commits

Commits on Sep 27, 2024

NEW: intrude edge params to a tree object
YapengLang
committed
ENH: attach rate and motif params to tree object for non-lie model
YapengLang
committed
TST: add tests for tree params
YapengLang
committed
MAINT: formatting
YapengLang
committed
ENH: reform rate pars to be consistent with cogent3
YapengLang
committed
TST: added test for the parameters when fit_tree are called
YapengLang
committed
TST: modified tests for corresponding rate parameters
YapengLang
committed
ENH: splitted function for processing yaml and reforming pars
YapengLang
committed
TST: modified tests for yaml processing
YapengLang
committed
MAINT: changed names of functions and commented
YapengLang
committed
TST: restricted the values for checking parameters fits
YapengLang
committed
TST: added type annotations for tree yaml tests
YapengLang
committed
MAINT: renamed `_format_edge_pars` and included type casting when processing yaml
YapengLang
committed
TST: modified test for cogent3 tree edge params
YapengLang
committed
TST: changed the relative tolerance as 1e-2 for rate parameters comparison between cogent3 and iqtree
YapengLang
committed

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