Should we Ignore heterozygous SNPs while constructing SNP based phylogeny

Question

[Optimist]

Hello!

Should we ignore heterozygous SNPs while constructing SNP based phylogeny for bacterial genomes. I'm Using CSI Phylogeny 1.4. CSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny based on the concatenated alignment of the high quality SNPs.

Thank You

Cheers

[karl.stamm]

heterozygous bacteria? heterozygous genotype in bacterial snp calling