Maxflow: source code, examples and installation
Heger et al. (2003) Accurate detection of very sparse sequence motifs. RECOMB 2003.
Maxflow - a program for the alignment of protein sequences based on pairwise consistency.
Follow this link for the GTG Server.
© 2003 Liisa Holm & Andreas Heger
Maxflow source code:
Files for running through a small example of Maxflow usage (8 sequences):
Files for running through a large, intensive example of Maxflow usage (399 sequences):
Maxflow is free software. Please see the file COPYING for details.
For documentation, please see the files in the doc/ subdirectory.
For building and installation instructions, read the INSTALL file.
PLEASE NOTE: you must have the alignlib library installed before you can install maxflow.
Author: Andreas Heger
How to run maxflow in a nutshell:
1. Installation:

        tar -xvzf maxflow-0.1.1.tgz
        cd maxflow-0.1.1
        ./configure --with-alignlib-dir=where_you_installed_alignlib \
                    --prefix=where_you_want_me_to_go
        make
        make install

2. Execution:

2.1 Input: build the residue graph

The residue graph has the following format:
node1   node2   some_ignored_number

where nodes have the format: protein-residue_number.

For example:

...
proteinA-12proteinB-150
proteinA-13proteinB-160
...
says that residue 12 and 13 in proteinA are aligned to 
residues 15 and 16 in proteinB, respectively. The 0 is a weight
and is currently not used.

2.2 run the program:
        cd example
	../src/maxflow -g edges -D proteinA proteinB

This will align proteinA with proteinB. There are more
alignment options available for doing a whole batch of
pairwise alignments based on a library of input sequences.

Download the examples to see maxflow in action.