reconcile-tree-alignment

Usage:

reconcile-tree-alignment <input tree> <input alignment> <output tree> <output alignment>

Description

Given a tree and an alignment, identify the intersection of the sets of sequence IDs and leaf labels. Trim the extra sequences and leaves and print the resulting alignment and tree.

Input

Input Tree

<input tree>

The name of a file containing a tree in Newick format.

<input alignment>

The name of a file containing a DNA or protein sequence alignment in clustalw format. The alignment can be read from standard input if a "-" is given instead of a file name.

<output tree>

The name of the file in which to save the reconciled Newick format tree.

<output alignment>

The name of the file in which to save the reconciled clustalw format sequence alignment.

Output

The reconciled versions of the tree and alignment are written out to the provided file names.