Dear Sonal,

As per the concept of molecular clock, i am quoting some lines from "Essential Bioinformatics" by Xiong, hope it will give you the basic understanding. The lines goes as follows:

"To define the direction of an evolution path, a tree must be rooted. In a

rooted tree, all the sequences under study have a common ancestor or root node from

which a unique evolutionary path leads to all other nodes. Obviously, a rooted tree is

more informative than an unrooted one. To convert an unrooted tree to a rooted tree,

one needs to first determine where the root is.

Strictly speaking, the root of the tree is not known; the common ancestor is already

extinct. In practice, however, it is often desirable to define the root of a tree. There are

two ways to define the root of a tree. One is to use an outgroup, which is a sequence

that is homologous to the sequences under consideration, but separated from those

sequences at an early evolutionary time. Outgroups are generally determined from

independent sources of information. For example, a bird sequence can be used as a

root for the phylogenetic analysis of mammals based on multiple lines of evidence

that indicate that birds branched off prior to all mammalian taxa in the ingroup.

Outgroups are required to be distinct from the ingroup sequences, but not too distant

from the ingroup. Using too divergent sequences as an outgroup can lead to errors in

tree construction. In the absence of a good outgroup, a tree can be rooted using the

midpoint rooting approach, in which the midpoint of the two most divergent groups

judged by overall branch lengths is assigned as the root. This type of rooting assumes

that divergence from root to tips for both branches is equal and follows the “molecular

clock” hypothesis.

Molecular clock is an assumption by which molecular sequences evolve at constant

rates so that the amount of accumulated mutations is proportional to evolutionary

time. Based on this hypothesis, branch lengths on a tree can be used to estimate

divergence time. This assumption of uniformity of evolutionary rates, however, rarely

holds true in reality."

To estimate the molecular clock tests you can use the below mentioned software

HYPHY (Reference: S.L. Kosakovsky et al.(2005) Bioinformatics 21:676-679).

Best wishes,

Amit

Thanxx amit...