Asymmetree

Latest version: v2.2.1

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2.2

New features

* the sampling of species trees can now be conditioned on the number of leaves and the age of the tree
* gene conversion is now supported as an event shaping the gene tree (in addition to duplication, loss, and HGT)
* additive and replacing HGT with transfer distance bias
* matplotlib-based visualization of trees now also accepts species trees as input

Changed

* the tree data structures are now in the package [tralda](https://github.com/david-schaller/tralda)
* the innovation model is now an option that modifies that sampling of species lineages for the next bifurcation rather than its own model
* the Gillespie mode (formerly jump chain) for sequence simulation now runs faster
* a number of functions have been re-named to be shorter and/or more meaningful, e.g. `observable_tree()` is now `prune_losses()`
* the reconciliation attribute of the gene tree nodes has been re-named from "color" to "reconc"

Fixed

* the distance attribute of the trees is now updated after contraction of edges to generate multifurcations
* evolution rate heterogeneity now correctly handles multifurcating duplication nodes

Removed

* the subpackage `paraphylo` was removed

0.1.0

AsymmeTree now supports the simulation of nucleotide and amino acid sequences, as well as the generation of genomes/proteomes.

0.0.5

0.0.1

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