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subtree (phytree)

Extract phylogenetic subtree

Syntax

Tree2 = subtree(Tree1, Nodes)

Description

Tree2 = subtree(Tree1, Nodes) extracts a new subtree (Tree2) where the new root is the first common ancestor of the Nodes vector from Tree1. Nodes in the tree are indexed as [1:NUMLEAVES] for the leaves and as [NUMLEAVES+1:NUMLEAVES+NUMBRANCHES] for the branches. Nodes can also be a logical array of following sizes [NUMLEAVES+NUMBRANCHES x 1], [NUMLEAVES x 1] or [NUMBRANCHES x 1].

Examples

  1. Load a phylogenetic tree created from a protein family.

    tr = phytreeread('pf00002.tree');
  2. Get the subtree that contains the VIPR2 and GLR human proteins.

    sel = getbyname(tr,{'vipr2_human','glr_human'});
    sel = any(sel,2);
    tr =  subtree(tr,sel);
    view(tr)

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