I'm part of a nanopore sequencing experiment that will sequence several generations of viruses. The intent is to perform directed evolution by putting selective pressure on these viruses and tracking the various mutations that occur. See here for the paper this methodology is based on.
I've been working on a software package that can compile consensus sequences from longread nanopore sequencing (see here). However, there's a wrinkle with generating phylogenetic trees from this type of data. It appears that most tree building software ignores indels. This makes sense, as gaps could easily indicate a lack of coverage from illumina sequencing methods or similar issues rather than betray the existence of an insertion/deletion. However, the nature of our sequencing method is such that a gaps really should be evaluated as mutational changes that we want to keep track of in a phylogenetic tree.
We've explored using NextStrain to generate our trees and visuals, but the tree building algorithms they employ too suffer from this gap assumption (see the issue I raised here). These include IQTree, RAxML and PhyML. I have not had much luck finding an algorithm or software that treats gaps as indels when building a phylogenetic tree. Does anyone know of such an algorithm or package I could employ? I figure I could take a stab at writing my own algorithm, but consider that a Plan B resort. No sense re-inventing the wheel and all that.