reconcile-tree-alignment <input tree> <input alignment> <output tree> <output alignment>
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.
A tree in Newick format.
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.
The file name to save the reconciled Newick format tree.
The file name to save the reconciled clustalw format sequence alignment.
The reconciled versions of the tree and alignment are written out to the provided file names.