pylogeny.tree module

Container definition for (phylogenetic) bifurcating or multifurcating trees defined using Newick strings, collections of them, and for splits of these trees.

class pylogeny.tree.bipartition(topol, bra=None)

Bases: object

A tree bipartition. Requires a tree topology. Using the term borrowed from nomenclature of a bipartite graph, a bipartition for a phylogenetic tree coincides with the definition of two disjoint sets U and V . A branch in a phylogenetic tree defines a single bipartition that divides the tree into two disjoint sets U and V . The set U comprises all of the children leaf of the subtree associated with that branch. The set V contains the rest of the leaves or taxa in the tree.

__init__(topol, bra=None)

Construct a bipartition from a branch in a topology.

Parameters:

• topol (rearrangement.topology) – A topology.
• bra (newick.branch) – An optional branch object.

fromStringRepresentation(st)

Acquire all component elements from a string representation of a bipartition.

Parameters:st – A string representation from a tree.bipartition object.

getBestSPRScore(ls, node=None)

Given a landscape, return the best SPR score.

getBranch()

Get branch corresponding to this bipartition.

Returns:newick.branch

getBranchIndex()

Return an index of the branch with respect to a post order traversal of the topology.

Returns:an integer

getBranchListRepresentation()

Get the tuple of lists of branches that represent this bipartition.

getMedianSPRScore(ls, node=None)

Given a landscape, return the median SPR score.

getSPRRearrangements()

Return the set of all scores related to this bipartition.

getSPRScores(ls, node=None)

Given a landscape, return all possible scores, not actively performing scoring if not done.

getShortStringMappings()

Get the mapping of symbols from taxa names for the shorter string representation.

getShortStringRepresentation()

Get the shorter string representation corresponding to this bipartition.

Returns:a string

getStringRepresentation()

Get the string representation corresponding to this bipartition.

Returns:a string

pylogeny.tree.median(lst)

pylogeny.tree.numberRootedTrees(t)

pylogeny.tree.numberUnrootedTrees(t)

class pylogeny.tree.tree(newi='', check=False, structure=None)

Bases: object

Represents a single (phylogenetic) tree by Newick string; can possess other metadata. For manipulation of tree structure, such as rerooting and unrooting, convert this object to a topology.

__init__(newi='', check=False, structure=None)

If enabled, “check” will force the structure to reroot the given Newick string tree to a lowest-order leaf in order to ensure a consistent Newick string among any duplicate topologies. If a structure is provided and check is disabled, all parsing routines are bypassed and the Newick and Structure fields of this tree are overriden by the appropriate arguments.

Parameters:

• newi (a string) – a Newick or New Hampshire string for a tree
• check (a boolean) – perform parsing checks on the string input

getName()

Gets the name of this tree if it has been defined.

Returns:a string

getNewick()

Gets the Newick (New Hampshire) string for this tree.

Returns:a string

getOrigin()

Gets the “origin” of this tree, or where this tree was acquired or constructed from. Usually set by other code or an interface.

Returns:string or None

getRerootedNoBranchLengthNewick()

Returns the tree’s “structure”, a Newick string without any branch lengths.

Returns:a string

getScore()

Gets the score(s) (objective function) for this tree if it/they has/have been defined.

Returns:a tuple of floats or integers

getSimpleNewick()

Return a Newick string with all taxa name replaced with successive integers.

Returns:a string

getStructure()

Returns the tree’s “structure”, a Newick string without any branch lengths.

Returns:a string

setName(n)

Sets the name of this tree (object).

Parameters:n (a string) – a string indicating this tree’s name

setOrigin(o)

Set the “origin” or specification of where this tree was acquired or constructed from.

Parameters:o (string or None) – a string indicating where the tree came from

setScore(s)

Sets the score(s) for this tree. Should be performed by a scorer (see scoring functions in the appropriate module).

Parameters:s (a tuple of floats or integers) – a set of objective function scores.

toDendroPy()

Convert the tree object to a DendroPy tree object. Requires DendroPy to be installed on the system.

Returns:a DendroPy Tree object or None if DendroPy not on system

toNewick()

Gets the Newick (New Hampshire) string for this tree.

Returns:a string

toTopology()

Return a topology object instance for this tree to allow for rearrangement of the actual structure of the tree.

Returns:a rearrangement.topology object

updateNewick(n, reroot=False)

Update the contained Newick string only as long as the structure obtained (after rerooting, which is an optional parameter) is identical to the contained structure.

Parameters:

• n (a string) – A Newick or New Hampshire formatted string.
• reroot (a boolean) – reroot to lexicographically lowest-order leaf.

class pylogeny.tree.treeSet

Bases: _abcoll.Sized, _abcoll.Iterable

Represents an ordered, disorganized collection of trees that do not necessarily comprise a combinatorial space.

__init__()

addTree(tr)

Add a tree object to the collection.

Parameters:tr (tree.tree) – A tree object.

addTreeByNewick(newick)

Add a tree to the structure by Newick string.

Parameters:newick (a string) – A New Hampshire or Newick string.

static fromTreeFile(fin)

Acquire a file where newlines separate Newick strings, and create an instance of treeSet from those trees.

indexOf(tr)

Acquire the index in this collection of a tree object. Returns -1 if not found.

Parameters:tr (tree.tree) – A tree object. Returns:an integer [-1,length of collection)

iterTrees()

Iterate over all trees found in this set.

removeTree(tr)

Remove a tree object from the collection if present.

Parameters:tr (tree.tree) – A tree object (present in the collection).

toTreeFile(fout)

Output this landscape as a series of trees, separated by newlines, as a text file saved at the given path.

Parameters:fout (a string) – A string indicating a file system path to a file.