Sorry in advance if my problem is very simple, I am only starting using R! :) Thanks a lot for your help in advance.
I have a bunch of DNA sequence alignments in FASTA format (~150 sequences, aligned, sometimes with gaps) and a corresponding phylogeny that I would like to use to calculate consistency indices (CI) in order to have a rough idea for homoplasy in various sequences of interest.
For this, I saw that I can use the CI() function from the R package phangorn. Below is what I do, but there is a problem as the R session aborts (bomb) as soon as I start running the last line below, either on my local machine or a large cluster with lots of RAM:
seqdata = read.FASTA(file="multifasta.fasta") seqdataPhy = phyDat(seqdata, type="DNA") phyloTree = read.tree(file="tree.nwk") CI(phyloTree, seqdataPhy)
I suspect something goes wrong when I try to create the sequence alignment data file in phyDat format (maybe I am forgetting some options?), but I haven't found any documentation on what I would like to do, so I try here. Thanks a lot, I am grateful for any advice!
All the best,