divergence time estimation

[Alim Junaid]

Hi everyone

I am a new user of paml package. I am calculating divergence time. For this single copy orthologs were aligned and then a phylogenetic tree was constructed. But when I am using this phylogenetic tree and aligned sequences in codeml, I am not getting the substitution rate in final output file for subsequent mcmtree analysis.  In this group someone have suggested to add '@4.5'; at the end of tree file. What is this parameter ? when I used this parameter in my tree file, I got the substitution rate.  Can anyone explain this parameter?

My tree file is in newick format

12 1
(O.sativa, (A.thaliana, (A.durensis, ((M.truncatula, C.arientum), (C.cajan, (G.max, (P.vulgaris, (V.ungiculata, (V.angularis, (V.mungo, V.radiata))))))))));

[Sishuo Wang]

That value should be a rough estimate of the root age before you do the analysis. Also, you may wish to pay attention to its unit when using mcmctree.