Hi, I'm dealing with WES samples consist of primary tumor, metastases(lymph nodes), normal from one patient.
I want to construct a phylogenetic tree using somatic SNVs. A binary data is used with normal sample as outgroup and for all somatic mutations found in the patient, if that specific somatic mutation exists in each metastases, it would be stated as 1(presense) and if it doesn't exists, it would be stated as 0(absense). My ultimate goal is to figure out which lymph node metastases first.
I notice that the PHYLIP program offers diverse methods. I'm thinking of using either 'pars' or 'penny' as the method but couldn't choose which one I should use. I personally think the assumption that penny uses (Changes 0 --> 1 are much more probable than changes 1 --> 0) is more consistent with the generally accepted theory of clonal progression in tumors. However, when I look through research articles that used PHYLIP, pars(Changes to all other states are equally probable (Wagner)) is way more commonly used and articles with 'penny' is hard to find.
Therefore, I am asking for help regarding this issue. Which method should I use for my tumor samples to construct a phylogenetic tree.