In this example we will use the PATHd8 program to put dates onto molecular trees. The method is described in the paper Estimating Divergence Times in Phylogenetic Trees Without a Molecular Clock (doi:10.1080/10635150590947311). Given a molecular tree we put dates on node using the concept of the "most recent common ancestor" or MRCA. We pick two leaves (terminal taxa) and add the date for their MRCA.
For example, to say that the common ancestor of mammals in the tree below is 100 million years old, we can say "the MRCA of rat and platypus has an age of 100 Mya".
In the exercise below we will put dates on nodes in the tree then create an ultrametric tree (i.e., a clock-like tree). A good source of dates for MRCA's is TimeTree.
To add dates you can pick two pairs of taxa and add the date they last had a common ancestor. The date for the first pair is taken as a fixed date, the rest are minimum dates.
(((EELA:0.150276,CONGERA:0.213019):0.230956,(EELB:0.263487,CONGERB:0.202633):0.246917):0.094785,((CAVEFISH:0.451027,(GOLDFISH:0.340495,ZEBRAFISH:0.390163):0.220565):0.067778,((((((NSAM:0.008113,NARG:0.014065):0.052991,SPUN:0.061003,(SMIC:0.027806,SDIA:0.015298,SXAN:0.046873):0.046977):0.009822,(NAUR:0.081298,(SSPI:0.023876,STIE:0.013652):0.058179):0.091775):0.073346,(MVIO:0.012271,MBER:0.039798):0.178835):0.147992,((BFNKILLIFISH:0.317455,(ONIL:0.029217,XCAU:0.084388):0.201166):0.055908,THORNYHEAD:0.252481):0.061905):0.157214,LAMPFISH:0.717196,((SCABBARDA:0.189684,SCABBARDB:0.362015):0.282263,((VIPERFISH:0.318217,BLACKDRAGON:0.109912):0.123642,LOOSEJAW:0.3971):0.287152):0.140663):0.206729):0.222485,(COELACANTH:0.558103,((CLAWEDFROG:0.441842,SALAMANDER:0.299607):0.135307,((CHAMELEON:0.771665,((PIGEON:0.150909,CHICKEN:0.172733):0.082163,ZEBRAFINCH:0.099172):0.272338):0.014055,((BOVINE:0.167569,DOLPHIN:0.15745):0.104783,ELEPHANT:0.166557):0.367205):0.050892):0.114731):0.295021);