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.
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[, exportattrs])	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.

Classes

RosettaTree(tree[, validate])

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

Modules

alifedata_phyloinformatics_convert.RosettaTree(tree)	Adapter class for implicit conversion between tree representations across phylogenetic libraries.
alifedata_phyloinformatics_convert.alife_dataframe_to_biopython_tree(df)	Open a phylogeny dataframe formatted to the artificial life community data format standards as a biopython tree.
alifedata_phyloinformatics_convert.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.
alifedata_phyloinformatics_convert.alife_dataframe_to_dendropy_tree(df)	Open a phylogeny dataframe formatted to the artificial life community data format standards as a dendropy tree.
alifedata_phyloinformatics_convert.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.
alifedata_phyloinformatics_convert.alife_dataframe_to_dict_of_lists(df)	Extract an adjacency representation for an alife standard dataframe.
alifedata_phyloinformatics_convert.alife_dataframe_to_ete_tree(df)	Open a phylogeny dataframe formatted to the artificial life community data format standards as a ete tree.
alifedata_phyloinformatics_convert.alife_dataframe_to_ete_trees(df)	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.
alifedata_phyloinformatics_convert.alife_dataframe_to_networkx_digraph(df)	Open a phylogeny dataframe formatted to the artificial life community data format standards as a networkx directed graph.
alifedata_phyloinformatics_convert.alife_dataframe_to_phylotrack_systematics(df)	Open a phylogeny dataframe formatted to the artificial life community data format standards as a phylotrackpy Systematics object.
alifedata_phyloinformatics_convert.anytree_tree_to_alife_dataframe(tree)	Convert a anytree tree to a dataframe formatted to the artificial life community data format standards.
alifedata_phyloinformatics_convert.biopython_tree_to_alife_dataframe(tree)	Convert a biopython phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.
alifedata_phyloinformatics_convert.cli
alifedata_phyloinformatics_convert.dendropy_tree_to_alife_dataframe(tree)	Convert a dendropy phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.
alifedata_phyloinformatics_convert.dendropy_tree_to_scipy_linkage_matrix(tree)	Create a SciPy linkage matrix from a DendroPy Tree object.
alifedata_phyloinformatics_convert.ete_tree_to_alife_dataframe(tree)	Convert a ete phylogenetic tree to a dataframe formatted to the artificial life communit data format standards.
alifedata_phyloinformatics_convert.networkx_digraph_to_alife_dataframe(graph)	Convert a networkx digraph to a dataframe formatted to the artificial life community data format standards.
alifedata_phyloinformatics_convert.phylotrack_systematics_to_alife_dataframe(...)	Convert a phylotrackpy Systematics object to a dataframe formatted to the artificial life community data format standards.
alifedata_phyloinformatics_convert.scipy_linkage_matrix_to_dendropy_tree(matrix)	Create a DendroPy Tree object from a SciPy linkage matrix.