Phylogenetics with Bio.Phylo — Biopython 1.85.dev0 documentation (2024)

Coloring branches within a tree

The function draw supports the display of different colors andbranch widths in a tree. As of Biopython 1.59, the color andwidth attributes are available on the basic Clade object and there’snothing extra required to use them. Both attributes refer to the branchleading the given clade, and apply recursively, so all descendentbranches will also inherit the assigned width and color values duringdisplay.

In earlier versions of Biopython, these were special features ofPhyloXML trees, and using the attributes required first converting thetree to a subclass of the basic tree object called Phylogeny, from theBio.Phylo.PhyloXML module.

In Biopython 1.55 and later, this is a convenient tree method:

>>> tree = tree.as_phyloxml()

In Biopython 1.54, you can accomplish the same thing with one extraimport:

>>> from Bio.Phylo.PhyloXML import Phylogeny>>> tree = Phylogeny.from_tree(tree)

Note that the file formats Newick and Nexus don’t support branch colorsor widths, so if you use these attributes in Bio.Phylo, you will only beable to save the values in PhyloXML format. (You can still save a treeas Newick or Nexus, but the color and width values will be skipped inthe output file.)

Now we can begin assigning colors. First, we’ll color the root cladegray. We can do that by assigning the 24-bit color value as an RGBtriple, an HTML-style hex string, or the name of one of the predefinedcolors.

>>> tree.root.color = (128, 128, 128)

Or:

>>> tree.root.color = "#808080"

Or:

>>> tree.root.color = "gray"

Colors for a clade are treated as cascading down through the entireclade, so when we colorize the root here, it turns the whole tree gray.We can override that by assigning a different color lower down on thetree.

Let’s target the most recent common ancestor (MRCA) of the nodes named“E” and “F”. The common_ancestor method returns a reference to thatclade in the original tree, so when we color that clade “salmon”, thecolor will show up in the original tree.

>>> mrca = tree.common_ancestor({"name": "E"}, {"name": "F"})>>> mrca.color = "salmon"

If we happened to know exactly where a certain clade is in the tree, interms of nested list entries, we can jump directly to that position inthe tree by indexing it. Here, the index [0,1] refers to the secondchild of the first child of the root.

>>> tree.clade[0, 1].color = "blue"

Finally, show our work:

>>> Phylo.draw(tree)

See Fig. 7.

Note that a clade’s color includes the branch leading to that clade, aswell as its descendents. The common ancestor of E and F turns out to bejust under the root, and with this coloring we can see exactly where theroot of the tree is.

My, we’ve accomplished a lot! Let’s take a break here and save our work.Call the write function with a file name or handle — here we usestandard output, to see what would be written — and the formatphyloxml. PhyloXML saves the colors we assigned, so you can openthis phyloXML file in another tree viewer like Archaeopteryx, and thecolors will show up there, too.

>>> import sys>>> n = Phylo.write(tree, sys.stdout, "phyloxml") <phyloxml ...> <phylogeny rooted="true"> <clade> <color> <red>128</red> <green>128</green> <blue>128</blue> </color> <clade> <clade> <clade> <name>A</name> </clade> <clade> <name>B</name> </clade> </clade> <clade> <color> <red>0</red> <green>0</green> <blue>255</blue> </color> <clade> <name>C</name> </clade> ... </clade> </phylogeny></phyloxml>>>> n1

The rest of this chapter covers the core functionality of Bio.Phylo ingreater detail. For more examples of using Bio.Phylo, see the cookbookpage on Biopython.org:

http://biopython.org/wiki/Phylo_cookbook

Search and traversal methods

For convenience, we provide a couple of simplified methods that returnall external or internal nodes directly as a list:

get_terminals

makes a list of all of this tree’s terminal (leaf) nodes.

get_nonterminals

makes a list of all of this tree’s nonterminal (internal) nodes.

These both wrap a method with full control over tree traversal,find_clades. Two more traversal methods, find_elements andfind_any, rely on the same core functionality and accept the samearguments, which we’ll call a “target specification” for lack of abetter description. These specify which objects in the tree will bematched and returned during iteration. The first argument can be any ofthe following types:

• A TreeElement instance, which tree elements will match byidentity — so searching with a Clade instance as the target will findthat clade in the tree;

• A string, which matches tree elements’ string representation — inparticular, a clade’s name (added in Biopython 1.56);

• A class or type, where every tree element of the same type(or sub-type) will be matched;

• A dictionary where keys are tree element attributes and valuesare matched to the corresponding attribute of each tree element. Thisone gets even more elaborate:

  • If an int is given, it matches numerically equal attributes,e.g. 1 will match 1 or 1.0

  • If a boolean is given (True or False), the corresponding attributevalue is evaluated as a boolean and checked for the same

  • None matches None

  • If a string is given, the value is treated as a regular expression(which must match the whole string in the corresponding elementattribute, not just a prefix). A given string without specialregex characters will match string attributes exactly, so if youdon’t use regexes, don’t worry about it. For example, in a treewith clade names Foo1, Foo2 and Foo3,tree.find_clades({"name": "Foo1"}) matches Foo1,{"name": "Foo.*"} matches all three clades, and{"name": "Foo"} doesn’t match anything.

  Since floating-point arithmetic can produce some strange behavior, wedon’t support matching floats directly. Instead, use theboolean True to match every element with a nonzero value in thespecified attribute, then filter on that attribute manually with aninequality (or exact number, if you like living dangerously).

  If the dictionary contains multiple entries, a matching element mustmatch each of the given attribute values — think “and”, not “or”.

• A function taking a single argument (it will be applied to eachelement in the tree), returning True or False. For convenience,LookupError, AttributeError and ValueError are silenced, so thisprovides another safe way to search for floating-point values in thetree, or some more complex characteristic.

After the target, there are two optional keyword arguments:

terminal

— A boolean value to select for or against terminal clades (a.k.a.leaf nodes): True searches for only terminal clades, False fornon-terminal (internal) clades, and the default, None, searches bothterminal and non-terminal clades, as well as any tree elementslacking the is_terminal method.

order

— Tree traversal order: "preorder" (default) is depth-firstsearch, "postorder" is DFS with child nodes preceding parents,and "level" is breadth-first search.

Finally, the methods accept arbitrary keyword arguments which aretreated the same way as a dictionary target specification: keys indicatethe name of the element attribute to search for, and the argument value(string, integer, None or boolean) is compared to the value of eachattribute found. If no keyword arguments are given, then any TreeElementtypes are matched. The code for this is generally shorter than passing adictionary as the target specification:tree.find_clades({"name": "Foo1"}) can be shortened totree.find_clades(name="Foo1").

(In Biopython 1.56 or later, this can be even shorter:tree.find_clades("Foo1"))

Now that we’ve mastered target specifications, here are the methods usedto traverse a tree:

find_clades

Find each clade containing a matching element. That is, find eachelement as with find_elements, but return the corresponding cladeobject. (This is usually what you want.)

The result is an iterable through all matching objects, searchingdepth-first by default. This is not necessarily the same order as theelements appear in the Newick, Nexus or XML source file!

find_elements

Find all tree elements matching the given attributes, and return thematching elements themselves. Simple Newick trees don’t have complexsub-elements, so this behaves the same as find_clades on them.PhyloXML trees often do have complex objects attached to clades, sothis method is useful for extracting those.

find_any

Return the first element found by find_elements(), or None. Thisis also useful for checking whether any matching element exists inthe tree, and can be used in a conditional.

Two more methods help navigating between nodes in the tree:

get_path

List the clades directly between the tree root (or current clade) andthe given target. Returns a list of all clade objects along thispath, ending with the given target, but excluding the root clade.

trace

List of all clade object between two targets in this tree. Excludingstart, including finish.

Information methods

These methods provide information about the whole tree (or any clade).

common_ancestor

Find the most recent common ancestor of all the given targets. (Thiswill be a Clade object). If no target is given, returns the root ofthe current clade (the one this method is called from); if 1 targetis given, this returns the target itself. However, if any of thespecified targets are not found in the current tree (or clade), anexception is raised.

count_terminals

Counts the number of terminal (leaf) nodes within the tree.

depths

Create a mapping of tree clades to depths. The result is a dictionarywhere the keys are all of the Clade instances in the tree, and thevalues are the distance from the root to each clade (includingterminals). By default the distance is the cumulative branch lengthleading to the clade, but with the unit_branch_lengths=Trueoption, only the number of branches (levels in the tree) is counted.

distance

Calculate the sum of the branch lengths between two targets. If onlyone target is specified, the other is the root of this tree.

total_branch_length

Calculate the sum of all the branch lengths in this tree. This isusually just called the “length” of the tree in phylogenetics, but weuse a more explicit name to avoid confusion with Python terminology.

The rest of these methods are boolean checks:

is_bifurcating

True if the tree is strictly bifurcating; i.e. all nodes have either2 or 0 children (internal or external, respectively). The root mayhave 3 descendents and still be considered part of a bifurcatingtree.

is_monophyletic

Test if all of the given targets comprise a complete subclade — i.e.,there exists a clade such that its terminals are the same set as thegiven targets. The targets should be terminals of the tree. Forconvenience, this method returns the common ancestor (MCRA) of thetargets if they are monophyletic (instead of the value True), andFalse otherwise.

is_parent_of

True if target is a descendent of this tree — not required to be adirect descendent. To check direct descendents of a clade, simply uselist membership testing: if subclade in clade: ...

is_preterminal

True if all direct descendents are terminal; False if any directdescendent is not terminal.

Modification methods

These methods modify the tree in-place. If you want to keep the originaltree intact, make a complete copy of the tree first, using Python’scopy module:

tree = Phylo.read("example.xml", "phyloxml")import copynewtree = copy.deepcopy(tree)

collapse

Deletes the target from the tree, relinking its children to itsparent.

collapse_all

Collapse all the descendents of this tree, leaving only terminals.Branch lengths are preserved, i.e. the distance to each terminalstays the same. With a target specification (see above), collapsesonly the internal nodes matching the specification.

ladderize

Sort clades in-place according to the number of terminal nodes.Deepest clades are placed last by default. Use reverse=True tosort clades deepest-to-shallowest.

prune

Prunes a terminal clade from the tree. If taxon is from abifurcation, the connecting node will be collapsed and its branchlength added to remaining terminal node. This might no longer be ameaningful value.

root_with_outgroup

Reroot this tree with the outgroup clade containing the giventargets, i.e. the common ancestor of the outgroup. This method isonly available on Tree objects, not Clades.

If the outgroup is identical to self.root, no change occurs. If theoutgroup clade is terminal (e.g. a single terminal node is given asthe outgroup), a new bifurcating root clade is created with a0-length branch to the given outgroup. Otherwise, the internal nodeat the base of the outgroup becomes a trifurcating root for the wholetree. If the original root was bifurcating, it is dropped from thetree.

In all cases, the total branch length of the tree stays the same.

root_at_midpoint

Reroot this tree at the calculated midpoint between the two mostdistant tips of the tree. (This uses root_with_outgroup under thehood.)

split

Generate n (default 2) new descendants. In a species tree, this isa speciation event. New clades have the given branch_length andthe same name as this clade’s root plus an integer suffix (countingfrom 0) — for example, splitting a clade named “A” produces thesub-clades “A0” and “A1”.

See the Phylo page on the Biopython wiki(http://biopython.org/wiki/Phylo) for more examples of using theavailable methods.

Features of PhyloXML trees

The phyloXML file format includes fields for annotating trees withadditional data types and visual cues.

See the PhyloXML page on the Biopython wiki(http://biopython.org/wiki/PhyloXML) for descriptions and examples ofusing the additional annotation features provided by PhyloXML.