Recent Releases of tact
tact - v0.5.0
- TACT has a new documentation website, available at tact.jonathanchang.org.
- Adds an experimental command,
tact_add_config. This uses a configuration-based approach to specify nodes of interest where unsampled species will be placed. This feature is currently undocumented and is expected to have many bugs. - Adds a
--versionoption to most commands. - Uses a new interval bounds checker to ensure that the union of all possible age constraints on a clade is itself an atomic (single) interval, rather than a disjunction of multiple such intervals.
- Checks for a valid taxonomy tree are moved from
tact_build_taxonomic_treetotact_add_taxa, ensuring that taxonomic trees generated outside of TACT can still be appropriately validated. - Drops support for Python 3.7.
- Adds support for Python 3.11.
- Updates NumPy to 1.24.
- Updates SciPy to 1.10.
- Updates DendroPy to 4.6.
- Updates the version of PyPy in the Docker image to use Python 3.9.
- Python
Published by jonchang almost 3 years ago
tact - v0.4.0
This minor release of TACT drops support for Python 3.6 (as the latest versions of numpy and scipy have also dropped Python 3.6 support) and introduces the --ultrametricity-precision option to control the precision of ultrametricity checks. The algorithm is similar to the is.ultrametric function in the R package ape. Note that node ages will be normalized be slightly older when the left child and right child's ages differ. See DendroPy's documentation of is_force_max_age for details.
- Python
Published by jonchang over 4 years ago
tact - v0.3.4
This release introduces a new dual-optimizer algorithm, which uses simulated annealing to estimate diversification rates when the standard optimizer fails. This should address optimization problems that occur when estimating parameters on particularly species-rich or species-poor groups. It was inspired by prior art in hisse and treePL.
- full python 3.9 support since scipy now has cp39 wheels
- skip trying to estimate rates for cherries as this never worked to begin with and would always use the ancestor rate anyway
- better reporting of which species in the backbone are breaking desired taxonomic monophyly
- Python
Published by jonchang over 5 years ago
tact - v0.3.0
Overhauls tact_build_taxonomic_tree in various ways
- Now doesn't care if its input is sorted
- Will automatically modify non-unique rank names to become unique
- Will detect and warn you of empty cells in your taxonomy spreadsheet
- Checks that the resultant phylogeny is actually valid
Also turns off a few annoying warnings in tact_add_taxa.
- Python
Published by jonchang over 5 years ago