extract_fasttree_constraints: Extract tree constraints in FastTree alignment format.

In castor: Efficient Phylogenetics on Large Trees

Extract tree constraints in FastTree alignment format.

Description

Given a rooted phylogenetic tree, extract binary constraints in FastTree alignment format. Every internal bifurcating node with more than 2 descending tips will constitute an separate constraint.

Usage

extract_fasttree_constraints(tree)

Arguments

tree	A rooted tree of class "phylo".

Details

This function can be used to define constraints based on a backbone subtree, to be used to generate a larger tree using FastTree (as of v2.1.11). Only bifurcating nodes with at least 3 descending tips are used as constraints.

The constraints are returned as a 2D matrix; the actual fasta file with the constraint alignments can be written easily from this matrix. For more details on FastTree constraints see the original FastTree documentation.

Value

A list with the following elements:

Nconstraints	Integer, specifying the number of constraints extracted.
constraints	2D character matrix of size Ntips x Nconstraints, with values '0', '1' or '-', specifying which side ("left" or "right") of a constraint (node) each tip is found on.
constraint2node	Integer vector of size Nconstraints, with values in 1,..,Nnodes, specifying the original node index used to define each constraint.

Author(s)

Stilianos Louca

Examples

# generate a simple rooted tree, with tip names tip.1, tip.2, ...
Ntips = 10
tree  = generate_random_tree(list(birth_rate_intercept=1),
                             max_tips=Ntips,
                             tip_basename="tip.")$tree

# extract constraints
constraints = castor::extract_fasttree_constraints(tree)$constraints

# print constraints to screen in fasta format
cat(paste(sapply(1:Ntips, 
    FUN=function(tip) sprintf(">%s\n%s\n",tree$tip.label[tip],
    paste(as.character(constraints[tip,]),collapse=""))),collapse=""))

castor documentation built on June 29, 2024, 9:08 a.m.