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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.
Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model.
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. [6]
The results are a phylogenetic tree—a diagram depicting the hypothetical relationships between organisms and their evolutionary history. [ 4 ] The tips of a phylogenetic tree can be living taxa or fossils , which represent the present time or "end" of an evolutionary lineage, respectively.
For example, in maximum parsimony analysis, there may be many trees with the same parsimony score. A strict consensus tree would show which nodes are found in all equally parsimonious trees, and which nodes differ. Consensus trees are also used to evaluate support on phylogenies reconstructed with Bayesian inference (see below).
The lower tree can be unrooted, multifurcating, or given as a sample of potential trees and reconciliation can be used to resolve those uncertainties to get a binary rooted lower tree. Reconciliation can also take as input non binary trees, that is, with internal nodes with more than two children. Such trees can be obtained for example by ...
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.
The multispecies coalescent results in cases where the relationships among species for an individual gene (the gene tree) can differ from the broader history of the species (the species tree). It has important implications for the theory and practice of phylogenetics [3] [4] and for understanding genome evolution.