I'm helping someone analyse rRNA ITS data from several
plant species. It contains short stretches that look like
microsatellites (e.g. GC---- in one species, GCGC-- and GCGCGCG
in others; "-" denotes gaps).
My feeling is to exclude thses stretches from the phylogenetic
tree analysis as they probably are microsatellites and thus
do not evolve by simple nucleotide substitution. The trouble
is that there is not a lot a variation left in the dataset if
these are excluded.
Is excluding them too drastic a solution?
BioSS, University of Edinburgh
frank at bioss.sari.ac.uk