RPoly v1.2.1
Haplotype Inference by Pure Parsimony (HIPP) using Pseudo-Boolean Optimization

by Ana Graca, Joao Marques-Silva, Ines Lynce, Arlindo Oliveira
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How to Run in Linux:
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You must have in the same directory two files:
rpoly and minisat+_64-bit_static
Then, type in the command line:

./rpoly <OPTIONS> filename
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Version 1.2.1 allows different options:

Solver options:
-t   <time>     Set a timeout (seconds) for MiniSat+. May return approximate solution
-n              Input-file nucleotides format instead of numbers format
-pbo            Write pseudo-Boolean optimization model in file rpoly.opb


TIMEOUT (option -t)
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This option requires that your system has the command 'timeout', normally available in unix!!!
'time' must be a positive integer.

If the timeout is reached, the solver returns an approximate solution to the pure parsimony.



NUCLEOTIDES FORMAT (option -n)
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RPoly accepts a new input format where:

- 'T','A','G','C' represent  homozygous sites
- 'H' represents a heterozygous site
- '?' represents an unknown site

Example:
r1 TTHHAH
r2 GHCC?H
r3 TGC?HH
r4 H??HHH
r5 HHHH?C