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Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree.
As shown by Felsenstein (1978), MP might be statistically inconsistent, [15] meaning that as more and more data (e.g. sequence length) is accumulated, results can converge on an incorrect tree and lead to long branch attraction, a phylogenetic phenomenon where taxa with long branches (numerous character state changes) tend to appear more ...
MEGA has created captions using the Real-Time Caption Editor to be able to analyze the properties of the results of the phylogenetic tree. This allows a user to be able to follow and interpret final results. [14] The Caption Expert is a part of MEGA which provides publication-like detailed captions based on the properties of analysis results.
Phylogenomics is the intersection of the fields of evolution and genomics. [1] The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. [2] It is a group of techniques within the larger fields of phylogenetics and genomics.
Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), [citation needed] usually an inputed sequence that is not represented in the input.
The simple phylogenetic tree of viruses A-E shows the relationships between viruses e.g., all viruses are descendants of Virus A. HIV forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples. Phylogenetic analysis has been used in criminal trials to exonerate or hold individuals.
By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons). The models described on this page describe the evolution of a single site within a set of sequences.
The "minimum evolution problem" (MEP), in which a minimum-summed-length phylogeny is derived from a set of sequences under the ME criterion, is said to be NP-hard. [13] [14] The "balanced minimum evolution problem" (BMEP), which uses the newer BME criterion, is APX-hard. [5] A number of exact algorithms solving BMEP have been described.