missing call in intratumor regions for phylogenetic analysis

Question

[Linda]

Hi there,

I am trying to create the phylogenetic tree for intratumoral regions using Wagner parsimony method in PHYLIP. Variant sites can be coded as 1/0 based on presence/absence of the mutation allele. However, there are missing calls in some intratumoral regions. For example, there are 8 intratumoral regions, but only one region was with missing calls. It is not proper to remove this variant site due to one missing call. I am wondering how to code this missing call in phylogenetic analysis? Thanks a lot!