Hello, everyone!

I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis.

I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in all isolates, & another that is 2 kb in length but only present in one-third of the isolates. I am wondering if I should include the second partition in my analysis, despite its incomplete nature.

I have found some publications discussing the use of incomplete data in phylogenetic analyses, such as Yuchi Zheng & John J. Wiens (2015), Rasmus Hovmöller et al. (2013), John J. Wiens & Jonathan Tiu (2012). However, I remain uncertain about the best course of action.

If you have experience working with incomplete data in BEAST analyses or any insights on this matter, I would greatly appreciate your advice.

Thank you in advance for your help.

Best regards, Pavel