Can anybody summarize the stepwise procedure of reconstructing a species tree involving protein sequences from 6 species? Although I found this Post useful in this regard, I'm still not able to understand how to arrange the protein sequences from each specie for the initial Multiple sequence alignment. It would be really helpful if I get a step wise procedure for species tree reconstruction. Thanks.
There is a nice list of tutorials on the BEAST webpage with step-by-step instructions. In particular, you may want to check out the *BEAST tutorial at the bottom of the page for species tree reconstruction (here is another *BEAST tutorial).
Another resource is the STRAW web server, which uses the STAR method. There is a nice description of the methods, and a walk through of the procedures on the help page of that site. I'm also aware of similar methods in HyPhy, which is available as an R package now.
These resources will help if know what you need to do but just need a short guide on some approaches. If you are unclear about the methods, I recommend reading Inferring Phylogenies by Joe Felsenstein, or The Phylogenetic Handbook by Lemey et al. for a much deeper description. In particular, those books cover the background on multiple alignments and the theory on tree construction.
If you are still looking for the tutorials, here is workshop materials that we designed as a basic phylogenetic tree reconstruction from whole genomes. Especially if you have no background in evolutionary genomics, then this will guide you step by step. Hope this will help!