Is there any NJ phylogenetic tree calculation method that would work on large genomic alignments and which takes into account/weight the gaps in the alignment?
I have managed to do it with FastTree, which does it exactly as I would like (from their website: "When comparing two sequences, positions with gaps are ignored; when comparing two profiles, positions are weighted by their proportions of non-gaps.") but I was wondering if there was a NJ method to do it as well. I use RapidNJ, which doesn't seem to be able to do it.
There is/was an option in MEGA to do it, by defining the gap threshold, i.e. the percentage of gaps required for each site to be considered, but I'd prefer a command-line based method as MEGA does not handle well large alignment files.
Thanks a lot for your help