Dear All (and esp. @Alexis_RAxML )
I’m working on a presentation for a meeting on microbial source attribution using genomic data, in which I am looking at datasets where sampled taxa are (or should be) located at internal nodes of the phylogeny. I’ve looked into family joining, and I know about the sampled ancestors work in BEAST (though I’ve been struggling with getting BEAST to fit the data), but I was wondering whether anyone had any experience with the -f C option in RAxML? The help said that it didn’t really work for real data, and I’m wondering whether anyone knows why, or has just tested it anyway.
Are there any other software packages that will collapse taxa to internal nodes?