Computational Phylogenetics
See also:
Phylogenetics and sequence alignment are closely related fields due
to the shared necessity of evaluating sequence relatedness. The field
of phylogenetics makes extensive use of sequence alignments in the construction and interpretation of phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes
of divergent species. The degree to which sequences in a query set
differ is qualitatively related to the sequences' evolutionary distance
from one another. Roughly speaking, high sequence identity suggests
that the sequences in question have a comparatively young most recent common ancestor, while low identity suggests that the divergence is more ancient. This approximation, which reflects the "molecular clock"
hypothesis that a roughly constant rate of evolutionary change can be
used to extrapolate the elapsed time since two genes first diverged
(that is, the coalescence time), assumes that the effects of mutation and selection
are constant across sequence lineages. Therefore it does not account
for possible difference among organisms or species in the rates of DNA repair
or the possible functional conservation of specific regions in a
sequence. (In the case of nucleotide sequences, the molecular clock
hypothesis in its most basic form also discounts the difference in
acceptance rates between silent mutations that do not alter the meaning of a given codon and other mutations that result in a different amino acid
being incorporated into the protein.) More statistically accurate
methods allow the evolutionary rate on each branch of the phylogenetic
tree to vary, thus producing better estimates of coalescence times for
genes.
Progressive multiple alignment techniques produce a phylogenetic
tree by necessity because they incorporate sequences into the growing
alignment in order of relatedness. Other techniques that assemble
multiple sequence alignments and phylogenetic trees score and sort
trees first and calculate a multiple sequence alignment from the
highest-scoring tree. Commonly used methods of phylogenetic tree
construction are mainly heuristic because the problem of selecting the optimal tree, like the problem of selecting the optimal multiple sequence alignment, is NP-hard.[18]
This article is licensed under the GNU Free Documentation License. It uses material from Wikipedia Encyclopedia article "Computational Phylogenetics"
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