Package `asymmetree`

AsymmeTree - Simulation of complex gene families

AsymmeTree is an open-source Python library for the simulation and analysis of phylogenetic scenarios. It includes a simulator for species and gene trees with heterogeneous evolution rates, nucleotide and amino acid sequences with or without indels, as well as whole genomes/proteomes.

Moreover, it includes a matplotlib-based visualization of the simulated trees as well as tools for the extraction of information from the simulated scenarios such as orthology, best matches, and xenology.

The library is primarily designed to explore and validate mathematical concepts, and to test inference methods for various steps on the way to more realistically-available data, i.e., dated gene trees, additive distances of gene sets, noisy distances and finally sequences.

Expand source code

# -*- coding: utf-8 -*-

"""AsymmeTree - Simulation of complex gene families

AsymmeTree is an open-source Python library for the simulation and analysis of
phylogenetic scenarios. It includes a simulator for species and gene trees with
heterogeneous evolution rates, nucleotide and amino acid sequences with or
without indels, as well as whole genomes/proteomes.

Moreover, it includes a matplotlib-based visualization of the simulated trees
as well as tools for the extraction of information from the simulated scenarios
such as orthology, best matches, and xenology.

The library is primarily designed to explore and validate mathematical concepts,
and to test inference methods for various steps on the way to more
realistically-available data, i.e., dated gene trees, additive distances of
gene sets, noisy distances and finally sequences.
"""

Sub-modules

asymmetree.analysis: Extraction and analysis of orthology, xenology, best matches, …
asymmetree.file_io: File I/O.
asymmetree.genome: Genome simulation …
asymmetree.seqevolve: Evolving sequences along trees …
asymmetree.tools: Tools for sampling, distance estimation, and tree analysis.
asymmetree.treeevolve: Simulation of species and gene trees …
asymmetree.visualize: Visualization of simulated species and gene trees.