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