     phyl2flat                                               update 24 Aug 07

     SYNOPSIS                                                  
           phyl2flat [-n -i -s] < Phylip_file > outfile                           
                                                             
     DESCRIPTION                                               
           Convert PHYLIP discrete data file into a GDE flatfile or 
	   sequential file. 
           See PHYLIP documentation (discrete.doc) for a formal
           definition of Phylip interleaved and sequential formats. 
	   phyl2flat is used by GDE to run import Phylip data, for use
	   with such as RESTML, NEIGHBOR, FITCH, KITSCH, DOLLOP, WAGNER etc. 
	   The -s option is needed to reformat molecular marker (0,1)
	   data as input for seqboot, which can only read marker data
	   in sequential format.
                                                 
          -n     Read non-interleaved (sequential) format.      
                                                             
          -i     invert characters, so that 0 -> 1 and 1 -> 0.   
	  -s     write output in Phylip sequential format  
                 (default: interleaved format)                                    
                                                                       

     EXAMPLE

          Given an input file in Phylip interleaved format:
          
          3       319
          G-A1      01001100110011000011100101011001001001011010000011
          G-A2      01001000110111010011101101010000000001111001001011
          G-A3      01000100110011000011100000011010101001011100111011
          11010000010111011011101001110101110001001100010011
          00010000000100111011101001100011110011011110011010
          00110000010100111011100011100011100011011101010010
          01000111111111011010101011100111111111000101100011
          00000110010111110100000010110101001100000000010111
          010001100101110000000010101001111111000???????????
          01101011000101110011110100110101111101000001010111
          01111011000100010101110000111101011100000001010011
          ??????????????????????????111101111000000001010011
          11010110001110011110000000001001101100001000000000
          11110111001111010110001010000001100010100000000111
          10010110001110010110001010001000101111011001101111
          00000000000000101011000101000101100100011000100001
          11111001011000000000000101000101100000011100011101
          01111000010000000010000101000001100100111000001101
          0000100000000010100
          0000101100001110100
          0000101100100010100
          
          phyl2flat < infile > outfile
          
          produces output in GDE flatfile text format:
          
          
          "G-A1
          010011001100110000111001010110010010010110100000111101000001
          011101101110100111010111000100110001001101000111111111011010
          101011100111111111000101100011011010110001011100111101001101
          011111010000010101111101011000111001111000000000100110110000
          100000000000000000000000101011000101000101100100011000100001
          0000100000000010100
          "G-A2
          010010001101110100111011010100000000011110010010110001000000
          010011101110100110001111001101111001101000000110010111110100
          000010110101001100000000010111011110110001000101011100001111
          010111000000010100111111011100111101011000101000000110001010
          000000011111111001011000000000000101000101100000011100011101
          0000101100001110100
          "G-A3
          010001001100110000111000000110101010010111001110110011000001
          010011101110001110001110001101110101001001000110010111000000
          0010101001111111000?????????????????????????????????????1111
          011110000000010100111001011000111001011000101000100010111101
          100110111101111000010000000010000101000001100100111000001101
          0000101100100010100

          phyl2flat -s < infile > outfile
          
          produces output in Phylip sequential format:
	  
	           3       319
	  G-A1       
	  01001100110011000011100101011001001001011010000011
	  11010000010111011011101001110101110001001100010011
	  01000111111111011010101011100111111111000101100011
	  01101011000101110011110100110101111101000001010111
	  11010110001110011110000000001001101100001000000000
	  00000000000000101011000101000101100100011000100001
	  0000100000000010100
	  G-A2       
	  01001000110111010011101101010000000001111001001011
	  00010000000100111011101001100011110011011110011010
	  00000110010111110100000010110101001100000000010111
	  01111011000100010101110000111101011100000001010011
	  11110111001111010110001010000001100010100000000111
	  11111001011000000000000101000101100000011100011101
	  0000101100001110100
	  G-A3       
	  01000100110011000011100000011010101001011100111011
	  00110000010100111011100011100011100011011101010010
	  010001100101110000000010101001111111000???????????
	  ??????????????????????????111101111000000001010011
	  10010110001110010110001010001000101111011001101111
	  01111000010000000010000101000001100100111000001101
	  0000101100100010100
          
                
     SEE ALSO
       flat2phyl
                 
     AUTHOR
       Dr. Brian Fristensky
       Dept. of Plant Science
       University of Manitoba
       Winnipeg, MB  Canada  R3T 2N2
       Phone: 204-474-6085
       FAX: 204-261-5732
       frist@cc.umanitoba.ca

