FAKII - A SUITE OF UNIX FILTERS FOR FRAGMENT ASSEMBLY
         Gene Myers  - Department of Computer Science
       The University of Arizona - Tucson, Arizona 85721
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These tools are ASCII oriented and build a graph of all the overlaps 
amongst a collection of FASTA formated fragments.  They produce a
number of alternate assemblies from the graph, display an overlap graph,
display an assembly both as a layout and as a multi-alignment showing
the consensus of the fragments, and produce a CAF file.
Filters are used as UNIX commands :

 ** create_graph
Creation of a graph with all gels present in the entry file
Usage: create_graph [-c] {e_limit:%f} {o_thresh:%f}
        {d_limit:%f} {-FASTA, -fasta, -EXP, -exp} {fragment file}
         > {graph}
  Exemple : create_graph 0.009 10. 0.0001  gel >graph

** add_to_graph
Addition of gels in a graph
Usage: add_to_graph [-c] {e_limit:%f} {o_thresh:%f}
        {d_limit:%f} {-FASTA, -fasta, -EXP, -exp} {fragment  file} 
        < {graph} > {graph}
  
** show_graph
Output of the graph
Usage : show_graph <graph

** assemble
Assmbly of gels in relation with the graph
Usage: assemble [-{i'th:%d}] [-c{constraints}] {e_rate:%f} 
       {o_thresh:%f} {d_thresh:%f} < {graph} > {assembly}
  Exemple : assemble 0.05 20. 0.0001 <graph  >assembly

** show_layout
Output of the overlaps in the contigs
Usage: show_layout [-c{contig:%d}] [-w{colums:%d}] [-z{scale:%d}]
       [-n]<assembly 
  Example : show_layout <assembly

** show_multi
Output of the gels with the consensus
Usage: show_multi [-c{contig:%d}] [-w{colums:%d}] [-m] <assembly
  Example : show_multi <assembly

** caf_multi
Export of multialignments as a CAF representation (compatible with tools as
GAP4 , PHRAP ..)
Usage: caf_multi [-c{contig:%d}] [-w{colums:%d}] <assembly
  Example : caf_multi <assembly

** create_exp_constraints
Usage: create_exp_constraints {constraint_binary_file} 
       {constraint_ascii_file} < {graph}

** write_exp_file
Usage: write_exp_file [-c contig] {-o output_directory} {-f output_fofn}
       < {assembly}

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