Here, I would like to get your helps on finding a computationally-effective tool to directly generate Maximum Likelihood phylogeny tree (rooted with outgroup). There would be many choice for constructing ML phylogeny tree. However, I have fewer experiences on this topic. So your advice/direction would be very valuable to me. I would like to know: which computational tool could I depend on? Advice on tools other than ML is also welcome.
My objective: In my study, I have sequences from several individuals of one species (in-group), and homologous sequences from one of another species (outgroup). I want to generate a ML phylogeny tree for in-group with outgroup as root.
Here I listed what I have tried: (1) PhyML (http://www.atgc-montpellier.fr/phyml/) It could be run parallel in multiple cores, and It could be run on-line. However, it could not directly output me a rooted tree with outgroup (see: http://www.atgc-montpellier.fr/phyml/faq.php). Setting up rooted tree from PhyML is not straightforward and usually ambiguously.
(2) nhphyml (http://pbil.univ-lyon1.fr/software/nhphyml/#OTHER_OPTIONS) Seems it could be a good choice. I did not implemented on my own data. I plan to try.
(3) PAML (baseml, http://abacus.gene.ucl.ac.uk/software/paml.html) I did not experienced it. By checking the its manual, it seems it is used to compare trees. I am not sure if it could be depended on in my study for a rooted phylogeny tree. Any directions?
Do you have any other experiences to share with me? Or any advice, or directions to me?
Thanks in advance.