run make -f Makefile.gcc

./CUTAL -s test.txt -o testoutput.out

./CUTAL -s test.txt -P 1 -b 3

./CUTAL -s test.txt -P 4 -b 3 -r 0.05

./CUTAL -s test.txt -p 345 -v 2

./CUTAL -s test.txt -B [0---3],[6---15],[17---20] -b 4

./CUTAL -s filename [Options]

-s filename Specifies the file from which to read sequence data. Files should be fully aligned and in PHYLIP format: http://scikit-bio.org/docs/0.2.3/generated/skbio.io.phylip.html This is the only argument that must be specified.

[-b int] (Default 2) Sets the maximum number of block partitions to attempt. CUTAL will attempt to find the optimal block partition (with respect to the problem(s) under consideration) with at most this many blocks.

[-P int] (Default 15) Sets which problems to solve. The last 4 bits of the binary expression of this number determine which of the problems {Max Homoplasy Score, Total Homoplasy Score, Max Homoplasy Ratio, Total Homoplasy Ratio} to solve. Thus, for example: -P 1 (= 0001) means solve Max Homoplasy Score -P 2 (= 0010) means solve Total Homoplasy Score -P 4 (= 0100) means solve Max Homoplasy Ratio -P 8 (= 1000) means solve Total Homoplasy Ratio

	-P 5	 (= 0101)  means solve and Max Homoplasy Score Max Homoplasy Ratio

	By default, this value is set to 15 (= 1111), so all four problems will be solved.

[-h int] If this value is specified and Max Homoplasy Score is one of the problems to be solved, CUTAL will also return the block partition with fewest blocks that has maximum homoplasy score at most int, if such a partition exists with at most the requested number of blocks).

[-H int] If this value is specified and Total Homoplasy Score is one of the problems to be solved, CUTAL will also return the block partition with fewest blocks that has total homoplasy score at most int, if such a partition exists with at most the requested number of blocks).

[-r int] If this value is specified and Max Homoplasy Ratio is one of the problems to be solved, CUTAL will also return the block partition with fewest blocks that has maximum homoplasy ratio at most int, if such a partition exists with at most the requested number of blocks).

[-R int] If this value is specified and Total Homoplasy Ratio is one of the problems to be solved, CUTAL will also return the block partition with fewest blocks that has total homoplasy ratio at most int, if such a partition exists with at most the requested number of blocks).

[-B string] Specifies an optional block partition to compare with the block partition(s) found by CUTAL. Must be a string of the form [a---b],[c---d], ... [y---z] Where a >= 0, z is at most the number of sites/characters -1, any block [a--b] satisfies a <= b, and any pair of consecutive blocks [a---b],[c---d] satisfies c > b. If this value is specified, CUTAL will return the max homoplasy score, total homoplasy score, max homoplasy ratio and total homoplasy ratio of the given block partition; furthemore it will compare this block partition with an optimal block partition (with respect to the problem(s) under consideration) that has the same number of blocks. (The comparision includes the 'average internal boundary error' of the two partitions, a measure of how much the two partitions disagree.) A warning will be given if the specified block partition contains a block with no informative sites, or if there exists an informative site not contained in any block.

[-v int] (Default 1) Specifies how 'verbose' CUTAL should be. If set to 0, CUTAL will return the optimal solution to each problem under consideration (as well as the solutions acheiving a certain desired value and/or comparisions to an input block partition, as specified by -h,-H,-r,-R and -B). If set to 1, CUTAL will also return the optimal solution(s) for each possible number of of blocks, up to the specified maximum. If set to 2, CUTAL will also return the homoplasy score and a parsimonious tree for each block in each partition.

[-o filename] (Default output.out) Specifies a file to which all output information should be written. Note that CUTAL appends to this file rather than overwriting; thus, calling CUTAL several times with the same output file will lead to that file containing reports from multiple experiments.

[-p int] (Default 1) Sets the randomization seed to be used by CUTAL.

-n, -N, -t Undocumented parameters used by Parsimonator. We recommend not touching these in case something breaks.