Table 1

Built-in functions and tree methods
Source Function Description
Bio.Phylo read Parse a file in the given format and return a single tree.
Bio.Phylo parse Iteratively parse a file and return each of the trees it contains.
Bio.Phylo write Write a sequence of trees to file in the given format.
Bio.Phylo convert Convert between two tree file formats.
Bio.Phylo draw Plot the given tree using matplotlib (or pylab).
Bio.Phylo draw_ascii Draw an ascii-art phylogram of the given tree.
Bio.Phylo draw_graphviz Display a tree or clade as a graph, using the graphviz engine.
Bio.Phylo to_networkx Convert a Tree object to a NetworkX graph object.
TreeMixin find_elements Find all tree elements matching the given attributes.
TreeMixin find_clades Find each clade containing a matching element.
TreeMixin find_any Return the first matching element found by find_elements, if any.
TreeMixin get_path List the clades directly between the current node and the target.
TreeMixin get_nonterminals List of all of the tree or clade’s internal nodes.
TreeMixin get_terminals List of all of the tree or clade’s “leaf” nodes.
TreeMixin trace List of all clade object between two targets in the tree/clade.
TreeMixin common_ancestor Most recent common ancestor (clade) of all the given targets.
TreeMixin count_terminals Count the number of terminal nodes within the tree.
TreeMixin depths Create a mapping of tree clades to depths (by branch length).
TreeMixin distance Calculate the sum of the branch lengths between two targets.
TreeMixin is_bifurcating Return True if tree downstream of node is strictly bifurcating.
TreeMixin is_monophyletic If the given terminals comprise a complete subclade, return the MRCA.
TreeMixin is_parent_of True if target is a descendent of the tree.
TreeMixin is_preterminal True if all direct descendents are terminal.
TreeMixin total_branch_length Calculate the sum of all the branch lengths in the tree.
TreeMixin collapse Deletes target from the tree, relinking its children to its parent.
TreeMixin collapse_all Collapse all the descendents of the tree, leaving only terminals.
TreeMixin ladderize Sort clades in-place according to the number of terminal nodes.
TreeMixin prune Prunes a terminal clade from the tree.
TreeMixin split Generate n (default 2) new descendants.
Tree, Clade is_terminal True if the node has no descendents.
Tree root_with_outgroup Reroot the tree with the specified outgroup clade.
Tree root_at_midpoint Reroot the tree at the midpoint between the two most distant terminals.
Tree format Serialize the tree as a string in the specified file format.
Tree as_phyloxml Convert the tree to its PhyloXML subclass equivalent.
Tree from_clade Create a new Tree object given a clade.
Tree randomized Create a randomized bifurcating tree, given a list of taxa.
Phylogeny to_alignment Construct an alignment from the aligned sequences in this tree.
chi2 cdf_chi2 χ2 cumulative distribution function, for log-likelihood ratio tests.
baseml read Parse a BASEML results file.
codeml read Parse a CODEML results file.
yn00 read Parse a yn00 results file.
_paml.Paml write_ctl_file Dynamically build a program-specific control file.
_paml.Paml read_ctl_file Parse a control file to create a program-specific class instance.
_paml.Paml print_options Print all of the program options and their current settings.
_paml.Paml set_options Set the value of a program option.
_paml.Paml get_option Return the value of a program option.
_paml.Paml get_all_options Return the current values of all the program options.
_paml.Paml run Run a PAML program and parse the results.

Public methods and functions provided in the Bio.Phylo module and sub-modules. An up-to-date version of this information is available at webcite.

Talevich et al.

Talevich et al. BMC Bioinformatics 2012 13:209   doi:10.1186/1471-2105-13-209

Open Data