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. |
Bio.Phylo.BaseTree | ||
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. |
Bio.Phylo.PhyloXML | ||
Phylogeny | to_alignment | Construct an alignment from the aligned sequences in this tree. |
Bio.Phylo.PAML | ||
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. |