How to find Homoplastic SNPs

Question

[konstantinkul]

Hi! Could somebody explain me methods (or software, scripts etc.) which are usually used for homoplastic SNPs detection in given pseudo-alignment of SNPs (pseudo-matrix) after comparison of several bacterial whole genomes? Theoretically I understand that homoplasy is sharing of identical charters(SNPs) states that cannot be explained by inheritance from the common ancestor of a group of taxa. I would be grateful for any advice!

[konstantinkul]

I've just visited my previouse question. So I found the answer. I use PAUP which use maximum parsimony method to find homoplastic SNPs.