alifedata_phyloinformatics_convert

Top-level package for alifedata-phyloinformatics-convert.

Functions

alife_dataframe_to_biopython_tree(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as a biopython tree.

alife_dataframe_to_biopython_trees(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as zero or more biopython trees, depending on the number of clades with no common ancestor.

alife_dataframe_to_dendropy_tree(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as a dendropy tree.

alife_dataframe_to_dendropy_trees(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as zero or more dendropy trees, depending on the number of clades with no common ancestor.

alife_dataframe_to_dict_of_lists(df)

Extract an adjacency representation for an alife standard dataframe.

alife_dataframe_to_ete_tree(df[, setattrs, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as a ete tree.

alife_dataframe_to_ete_trees(df[, setattrs, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as zero or more ete trees, depending on the number of clades with no common ancestor.

alife_dataframe_to_networkx_digraph(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as a networkx directed graph.

alife_dataframe_to_phylotrack_systematics(df)

Open a phylogeny dataframe formatted to the artificial life community data format standards as a phylotrackpy Systematics object.

alife_dataframe_to_treeswift_tree(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as a treeswift tree.

alife_dataframe_to_treeswift_trees(df[, ...])

Open a phylogeny dataframe formatted to the artificial life community data format standards as zero or more treeswift trees, depending on the number of clades with no common ancestor.

anytree_tree_to_alife_dataframe(tree, *[, ...])

Convert a anytree tree to a dataframe formatted to the artificial life community data format standards.

biopython_tree_to_alife_dataframe(tree[, ...])

Convert a biopython phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.

dendropy_tree_to_alife_dataframe(tree[, ...])

Convert a dendropy phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.

dendropy_tree_to_scipy_linkage_matrix(tree)

Create a SciPy linkage matrix from a DendroPy Tree object.

ete_tree_to_alife_dataframe(tree[, ...])

Convert a ete phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.

networkx_digraph_to_alife_dataframe(graph, *)

Convert a networkx digraph to a dataframe formatted to the artificial life community data format standards.

phylotrack_systematics_to_alife_dataframe(...)

Convert a phylotrackpy Systematics object to a dataframe formatted to the artificial life community data format standards.

scipy_linkage_matrix_to_dendropy_tree(matrix)

Create a DendroPy Tree object from a SciPy linkage matrix.

treeswift_tree_to_alife_dataframe(tree[, ...])

Convert a treeswift phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.

Classes

RosettaTree(tree[, validate])

Adapter class for implicit conversion between tree representations across phylogenetic libraries.

Modules

alifedata_phyloinformatics_convert.cli