I am trying to generate a phylogenetic tree of a certain enzyme (~160aa) which highly conserved throughout Eukarya. I am especially interested in its evolution in Metazoa. My problem is that no matter what I do I always end up with trees that are supported by low bootstrap values.
I work as follows: I collected 31aa seq from 31 species representing Bilateria (mostly Lophotrochozoa and Ecdysozoa but also Deuterostomia), Cnidaria, Ctenophora, Porifera and Placozoa. I have rooted the tree with the choanoflagellet Monosiga brevicollis.
I use MAFFT-linsi for alignment. I usually also use GUIDANCE with several cutoff values to eliminate unreliable columns.
I generate the tree using RAxML gui with the following settings:
ML + slow bootstrap, 1000 runs, 1000 replications, Protgamma LG (or JTT as protein model) + empirical frequencies.
Any idea what I can change/add in order to increase the bootstrap support of the tree? I am at a loss...