IMgc maximizes the inclusiveness score (I):
which gives the relative importance of retaining segregating sites (S) compared to chromosomal copies (C) You can set the α value here:
If you use IMgc, please cite us! August E. Woerner, Murray P. Cox, and Michael F. Hammer.
"Recombination-filtered genomic datasets by information maximization."
Bioinformatics 23.14 (2007): 1851-1853.
An example input file is found here: Download fasta file