TreeDM(PGOneI)
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Alignment independent phylogeny reconstruction: a sequential pattern mining method
version1.0 

To compile TreeDM you need GNU Make and GCC.


Usage: 
		./TreeDM [options] ...

options:
  -n   <int>   The minimal number of non_wildcard residues in the pattern to be reported
  -s   <float>   The minimal proportion of proteins haveing the pattern
  -m   <int>   The maximal length of wildcard in the patterns
  -i   <string>   The pathway and filename of sequences in fasta format
  -p   <string>   The pathway and filename of the PatternSpace filedefaults: ./ppfile
  -o   <string>   The pathway of the distance matrix(defaults: ./)
  -h/?   help pritn this message
  
  
Use TreeDM to generate a distance matrix for nerghbor-joining method

It's easy to use
Go to Makefile directory

    make 

Then

    ./TreeDM [options]

	
Output includes two parts: patterns_file and Distance_Matrix(DM.txt) file

Use DM.txt as input for nerghbor-joining method
You can get a phylogenetic tree

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Use PHYLIP(from http://evolution.genetics.washington.edu/phylip/getme-new1.html)
software_package(neighbor) to generate a phylogenetic tree. If you have the PHYLIP
installed. Use neighbor program to Generate a phylogenetic tree using:
  
  [path]/neighbor [path]/DM.txt   

See example for details