¶

Tree¶

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Tree(
   name = '', children = None, dist = 3.3e-05
)

Methods:

.add_child¶

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.add_child(
   node
)

readNewick¶

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.readNewick(
   tree_list, defaultBLen = 3.3e-05, normalizeInputBLen = 1.0
)

From a list of strings defining phylogenetic trees in newick format, returns a list of Tree instances containing the biartitions of the tree in a modularized form, suitable for comparisons with other trees.

Args

• tree_list (list) : list of trees in newick format.
• defaultBLen (float, optional) : default branch length. Defaults to 0.000033.
• normalizeInputBLen (float, optional) : value used to normalize branch lenghts. Defaults to 1.0.

Returns

• trees : list of Tree instances

prepareTreeComparison¶

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.prepareTreeComparison(
   t1, rooted = False, minimumBLen = 6e-06
)

Prepares newick tree for comparison

Args

• t1 (str) : input tree
• rooted (bool, optional) : set to True if t1 is rooted, default ro False
• minimumBLen (float, optional) : minimum value for branch length, default to 6E-6

Returns

• metrics (tuple of values) (leafNameDict, nodeTable, leafCount, numBranches, leafDistDict, branchLengthDict, sumBranchLengths,) : tree metrics among which the RFL.

RobinsonFouldsWithDay1985¶

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.RobinsonFouldsWithDay1985(
   t2, t1, rooted = False, minimumBLen = 6e-06
)

Computes Robison Foulds distances using Day's algorithm

Args

• t2 (string) : newick tree to be compared to t1
• t1 (tuple) : t1 after preprocessing using prepareTreeComparison()
• rooted (bool, optional) : True if t2 is rooted. Defaults to False.
• minimumBLen (float, optional) : minimum branch length. Defaults to 0.000006.

Returns

• parameters (tuple) (numDiffs, float(numDiffs) / (normalization), leafCount, foundBranches, missedBranches, (numBranches - foundBranches), RFL) : results of comparison, among which the RF distance (numDiffs).

calculate_distance_matrix¶

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.calculate_distance_matrix(
   file, n_trees, output_file
)

Computes the whole pipeline that calculates the pairwise distances in a collection of trees

Args

• file (str) : file containing the newick trees
• n_trees (int) : number of trees (or lines) in file
• output_file (str) : output file for distance matrix

Returns

• distance_matrix (np.array) : distance matrix