Any interest in a discussion about phylogenetics?

Just finished my Molecular Evolution course (aka. Phylogenetics) and was wondering if anyone is interested in having a discussion on phylogenetics. If so, respond to his post with any areas of interest you may have that could be discussed. Some examples of ideas might be:How to properly read and interpret phylogenetic treesHow to align DNA sequences and how alignments can influence resultsHow the types of analyses differ in their approach and what the weaknesses and strengths of each areWhat Bayesian analysis is and how it worksHow character mapping is done and how to interpret ancestral character states
___________I wouldn't say I am an expert in this area, but discussing it will help solidify the things I have learned and I also imagine that there is a fair amount of uncertainty and confusion regarding phylogenetic approaches out there and it may be helpful to discuss it. But... I don't want to just "preach" about things no one is interested in discussing.HBD* I will start a discussion in Biological Evolution if there is interest.Edited by herebedragons, : No reason given.

I received a couple cheers for this topic, but I was hoping to get some feedback on some aspects of the topic that people were interested in discussing.If there are some specific topics of interest, then please specify. I don't want to spend time if it will not generate discussion and have some purpose.HBD

I like this thread idea, and surely hope it will generate a considerable degree of interest from EvC members.Could you explain, in lay terms, what Bayesian analysis is? It's my favorite approach to phylogenetic analysis (scratch that: I prefer maximum-likelihood only as a matter of convenience since more programs AFAIK can generate maximum-likelihood phylogenies than Bayesian ones) since it's more accurate and robust than neighbor joining trees.I think that many EvC participants might have a vague understanding of molecular phylogenetics, but the nuances are more nebulous. And I suspect that Bayesian analysis is one of those areas of phylogenetics that most people here would not be familiar with. Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.

lay terms... Bayesian... explain... !! Wow, tough crowd Maximum-likelihood does have some advantages over Bayesian but a major disadvantage is a good ML analysis is much slower (surprisingly). The ML analysis for my final project was going to take 5 days plus another 5+ for bootstrapping using PAUP4.0. I ended up using PHyML and it took about 6 hours, but I wasn't as confident in the results.I used MrBayes (available as a free download) for my Bayesian analysis. It works really well and only took about 3 hours. Yea, I suspect Bayesian is not well understood. It is a difficult place to start though; I will need to present some background first.Thanks for the response.HBD