Phylogenetic tree

A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor. A phylogenetic tree is a form of a cladogram. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and edge lengths correspond to time estimates. Each node in a phylogenetic tree is called a taxonomic unit. Internal nodes are generally referred to as Hypothetical Taxonomic Units (HTUs) as they cannot be directly observed.

A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup - close enough to allow inference from sequence or trait data, but far enough to be a clear outgroup.
While unrooted phylogenetic trees can be generated from rooted ones by omitting the root from a rooted tree, a root cannot be inferred on an unrooted tree without either an outgroup or additional assumptions (for instance, about relative rates of divergence).

There are three main methods of constructing phylogenetic trees: distance-based methods such as neighbor-joining, parsimony-based methods such as maximum parsimony, and character-based methods such as maximum likelihood or Bayesian inference.
Tree-building methods can be assessed on the basis of several criteria:

• efficiency (how long does it take to compute the answer, how much memory does it need?)
• power (does it make good use of the data, or is information being wasted?)
• consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)
• robustness (does it cope well with violations of the assumptions of the underlying model?)
• falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)

Cladistics :- is a branch of biology that determines the evolutionary relationships between organisms based on derived similarities. It is the most prominent of several forms of phylogenetic systematics, which study the evolutionary relationships between organisms. Cladistics is a method of rigorous analysis, using "shared derived traits" of the organisms being studied. Cladistic analysis forms the basis for most modern systems of biological classification, which seek to group organisms by evolutionary relationships. In contrast, phenetics groups organisms based on their overall similarity, while approaches that are more traditional tend to rely on key characters (morphology). Willi Hennig (1913 - 1976) is widely regarded as the founder of cladistics.
As the end result of a cladistic analysis, treelike relationship-diagrams called "cladograms" are drawn up to show different hypotheses of relationships. A cladistic analysis can be based on as much or as little information as the researcher selects. Modern systematic research is likely to be based on a wide variety of information, including DNA-sequences (so called "molecular data"), biochemical data and morphological data.

A taxon:- (plural taxa), or taxonomic unit, is a grouping of organisms (named or unnamed). Once named, a taxon will usually have a rank and can be placed at a particular level in a hierarchy.