Bioinformatics Toolbox™

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 VIPS and CGRR human proteins.

   sel = getbyname(tr,{'vips_human','cgrr_human'});
   sel = any(sel,2);
   tr =  subtree(tr,sel)
   view(tr);

See Also

Bioinformatics Toolbox functions: phytree (object constructor)

Bioinformatics Toolbox methods of phytree object: get, getbyname, prune, select

std (DataMatrix)

sum (DataMatrix)