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Tree based alignment

This option allows the alignment to be performed in a manner similar to that described by Feng and Doolittle (1987). Rather than using a single order, the sequences are aligned according to a defined evolutionary tree. In my implementation, the tree can be obtained by running program ORDER, this produces two files, an order_file and a tree_file. The order file specifies an order that preserves the clustering of the sequences by similarity. The tree_file gives specific instructions to the program as to which comparisons to make and in which order.

For example, given four sequences A,B,C,D. the tree_file may specify that A and B should be aligned first, then C with D and finally the AB alignment is aligned with the CD alignment using average scores at each amino acid position.

Example command file.

Commands                                      Explanation number
--------                                      ------------------

output_file=globin_mult_tree.out              1.
mode=multiple                                 2.
matrix=file=ampsdir:md.mat                    3.
gap_penalty=8.0                               4.
constant = 8                                  5.
consplot=mz                                   6.
print_vertical=                               7.
seq_file=globin.seq                           8.
order_file=globin_pairs_tree.ord              9.
tree_file=globin_pairs.tree                  10.

This is the same as with the exception of two items.

order_file defines the cluster order. This is usually different to the 'simple' order defined in globin_pairs.ord.

tree_file defines the tree_file generated by program ORDER, or manually typed in.

The example output file from this run is globin_mult_tree.out.