SCEO

This is an implementation of the Single Cell Event Ordering algorithm that was described in J. De Bie et al., "Single cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukaemia".

Usage:
java -jar SCEO.jar input=input.txt output=output.txt N=n
with
input = input file containing tab delimited matrix with for each gene a (named) row and for each cell a (named) column with the values 1=event present, 0=event absent, -1=NA
output = output file with an enumeration of the most possible orders of events, preceded by a value indicating the probability of this option.
N = number of paths to be in the output