This is an example of the file format accepted by the program RecMin.exe. Site labels may be arbitrary strings of characters, separated by spaces. Following the site labels, each line represents a new sequence to be read in, and the types for each site are read in sequentially along a line. Sequences must be in binary 0-1 format with only two types at each site, and site data may be separated by spaces if wished (as in the second row here). Missing data should be indicated by the '?' character. Multiple datasets can be included in the same file if they are separated by two forward slashes as below; such a double slash also indicates the start of the data to be read in. For this example, the program returns minima of R_m=6, R_h=13 and R_m=9, R_h=17 with a maximal subset size 6, width 15 and unknown ancestral types, for the two datasets (these datasets show too much recombination for the other minimum R_s to be readily calculable here). To run on this data, type for example RecMin.exe testdata.txt testdata.out -t 0 -s 6 -w 15 -e 0 -d 3 In this case the output file will be the file testdata.out; see the file Readme.txt for more details on program parameters. (Unfortunately, the program does not handle genotype data.) // 0.0178 301 0.0508 0.0777 0.0821 0.0931 0.1763 0.1895 0.1937 0.1982 0.1989 0.1990 0.2191 0.2450 0.2560 0.3192 0.3781 0.4232 0.4279 0.4489 0.4620 0.4770 0.4990 0.5120 0.5181 Site1 0.5322 0.5375 0.5663 0.5812 0.5823 0.6038 0.6427 0.6635 0.6861 0.6919 0.6935 0.7016 0.7107 0.7153 0.7357 0.7456 0.7498 0.7847 0.8002 0.8281 0.9172 0.9368 0.9427 0.9528 00000000100110001100000001000010001111101011000000 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 000000100?00001011000???0?000010?00000000000001100 00000010000000101100000001000010100000000000001100 0000001000000010111100000100001010??00000000001110 01000100100100000000100001000010100000000000011100 0000000000000010111000000100001010000??00000001100 01000100100100000000000001000010000000000000001110 00000010000000100000000001000010001??1101001000000 10000000011000101100000001000010000000000100011100 00000010000000101110000001000010100000000000001110 10000000011000101100000001000010000000000100011101 001000?00000?????100000001000010100000000000001100 01001000011000101100000001000010001111101011000000 00000000100100001000000010101100100000010000101100 00000010000000101111000001000010100000000000001110 00100010000000101100000001000010100000000000001100 00100010000000101100000001000010100000000000001100 01010100100100000000000001000010001111101001011100 00000000100100001100100001000010100000000000011100 00000010000000101100000001000010100000000000001100 00100010000000101100000001000010100000000000001100 00000010000000101100000001000011100000000000001100 00000000011000101100000001000010100000000000001110 00100010000000101100000001000010100000000000001100 00000000000000101110000001000010100000000000001100 00000010000000101110000001000010001111101001000110 00000010000000101110000001000010100000000000001110 10000000011000101100000001000010000000000100011100 00100010000000101100000001000010100000000000001100 01000100000000101100000001000010100000000000001110 01000100100100000000000001000010011111101001000000 00000010000000101100000001000010100000000000001100 00000010000000101100000001000010100000000000001100 00000010000000101110000001000010100000000000001110 00100010000000101100000001000010100000000000001100 00100010000000101100000001000010100000000000001110 00000010000000100000000001000010001111101001000000 00000000100100001000000010101100100000010000101100 00100010000000101100000001000010100000000000001100 00100010000000101100000001000010100000000000001100 00000010000000100000000001000010001111101001000000 0101010010010000110000??01010010100000000000001110 000000000000001011100000??000010100000000000001100 00000001011000010000010001?00010001111000000001110 00000000000000101110000001000010100000000000001100 00000000000000101100000001000010001111101011001100 000000100000001000000000010000100011111010?1000000 010101001??10000000000000100001000111110100?000110 01000100100100000000000001000010011111101001000000 // 0.0114 0.0124 0.0767 0.0887 0.0915 0.1307 0.1348 0.1361 0.1603 0.2098 0.2115 0.2160 0.2165 0.2286 0.2369 0.2409 0.2519 0.2542 0.2816 0.3185 0.3234 0.3636 0.3929 0.4088 0.4264 0.4433 0.4713 0.4812 0.4855 0.5185 0.6340 0.7089 0.7700 0.7877 0.7929 0.8020 0.8722 0.8795 0.8799 0.8835 0.9227 0.9445 0.9560 0.9629 0.9675 0.9681 0.9713 0.9873 0.9892 0.9908 00011110110000000000111100000100001100000000001000 00011100110000011000110001011000110010001100110000 11011100110001100000110000000110100000000001000100 11011110110000000000111100000100001100000011100001 11011110100010001000001100000011100001000001000000 10011100110000000000111100000100001100000000001000 11011110100010001001001100000010100000000100100001 11011110010001100000110000000100001101000001000000 10011100110000000010111100000100001100000000001000 00011100110000011000110001011000110010001100110000 11111110100010001001001100000010100000000100100001 11011110010001100000110000000100001101000001000000 11011110100010001000001100000011100001000001000000 10011100100010001000110001010000110000000000001000 11011100110001100000110000000110100000000001000100 11011110100010001000001100000000110000000100100011 00011100110000011000110001011000110010001100110000 11111110100010001001001100000010100000000100100001 11011100110001100000110000000110100000000001000100 11011110100010001000001100000000110000000100100011 00000001011101100000110000000100001100000011100001 11011100110001100000110000000110100000000001000100 11011110110000000000111100000100001100000000001000 11011110100010001000001100000010001100000011000000 10011100110000000000111100000000110000000100100001 00011100110000011000111100000000101101000001000000 00000001011101100000110000000100001100000011000000 00011100110000011000111100000000110000000100100001 11011110110000000000111100000100001100000011100001 10011100110000000000111100000000110000000100100011 11011110110000000000111100000100001100000000001000 11011100110001100000110000000110100000000001000100 11011110010001100000110000000100001101000001000000 11011110100010001000001100010000001100010000000000 10011100110000000000111100000100001100000000001000 11011110100010001000001100010000001100010000000000 11011100110001100000110000100110100000000001000100 00000001010000000000111110000000110000000001000100 10011100110000000010111100000100001100000000001000 10011100110000000100111100000010100000000100100001 10011100110000000010111100000100001100000000001000 11011110100010001000001100000000110000000100100011 00011100110000011000111100000000110000000100100001 10011100110000000000111100000100001100000000001000 00000001011101100000110000000100110000000100100011 10011100110000000000111100000000110000100100100001 11011100110001100000110000000110100000000001000100 10011100110000000000111100000100001100000000001000 10011100110000000000111100000000001100000011000000 10011100110000000000111100000010100000000000000000