I am looking for a tool that could predict the ancestral sequence for the phylogenetic tree. I have heard about FastML and MEGA6.0. Can anyone help me understand what do the alphabets M, L etc at the nodes mean while predicting ancestral sequence using MEGA? the detailed text output tells the probability of occurrence of each amino acid at respective nodes but is there a way to get the sequence directly?
Yes, there are, for instance (are URLs):
bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-123
www.ncbi.nlm.nih.gov/pmc/articles/PMC3394241/
bioinformatics.oxfordjournals.org/content/26/1/130.full now at: ancestors.bioinfo.uqam.ca/
Recent reviews and experimental tests at:
www.nature.com/articles/ncomms12847
www.bx.psu.edu/miller_lab/dist/11_Blanchette.pdf
science.sciencemag.org/content/sci/suppl/2004/09/01/305.5689.1433.DC1/ugalde.SOM.pdf
www.ncbi.nlm.nih.gov/pmc/articles/PMC4512549/
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