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) is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships.

The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Work with protein electrophoresis began around 1956.

Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a clade.

In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material; a substantial sample of individuals of the target species or other taxon is used, however many current studies are based on single individuals.

Haplotypes of individuals of closely related, but different, taxa are also determined.

Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic.

The recent discovery of extensive horizontal gene transfer among organisms provides a significant complication to molecular systematics, indicating that different genes within the same organism can have different phylogenies.

In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: This is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example the insertion of a section of nucleic acid in one haplotype that is not present in another).

The difference between organisms is usually re-expressed as a percentage divergence, by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA that is sequenced.In general, these are considered superior for evolutionary studies, since the actions of evolution are ultimately reflected in the genetic sequences.At present, it is still a long and expensive process to sequence the entire DNA of an organism (its genome).A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution models) and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol Early attempts at molecular systematics were also termed as chemotaxonomy and made use of proteins, enzymes, carbohydrates, and other molecules that were separated and characterized using techniques such as chromatography.These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or bases in either DNA or RNA segments extracted using different techniques.Every living organism contains DNA, RNA, and proteins.

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