I have been days struggling with a phylogenetic tree of around 90 short sequences (domain based) whose support values for many branches are really low (<30 in many cases). I have noticed that aLRT supports are good and do not correlate with the bootstrapped result.
I was wondering if the number of replicates (100 in my case) could have an effect in short alignments (~250 sites) or if there is an alternative way to measure the support of some specific branches in very unstable alignments. Note that even small variations in the the software used to align the sequences lead to different topologies.
Any suggestion on how to address this type of problem?
ps. I am using phyml for the tree (4 rate categories), and mafft-linsi for the alg