# The MEME Suite

## Motif-based sequence analysis tools

## 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.