The tree topology
The lengths of the branches
The branching order of the tree
Nucleotide substitution rate
These would not affect maximum likelihood estimates of phylogenies when comparing different tree hypotheses.
<h3>What is tree topology?</h3>
- A unique kind of structure called a tree topology has numerous connected parts arranged like the branches of a tree.
<h3>The lengths of the branches:</h3>
- Branch lengths are a sign of genetic divergence; the longer the branch, the more genetic divergence has taken place.
- Usually, we calculate the average number of nucleotide or protein substitutions per site to assess the degree of genetic alteration.
<h3>The branching order of the tree:</h3>
- The topology of a tree refers to its branching structure.
- Species (or higher taxa), populations, genes, and proteins are examples of taxonomic units that the nodes represent.
- A branch is referred to as an edge, and it represents an estimate of the length of time between the evolutionary relationships between taxonomic units.
<h3>What is nucleotide substitution rate?</h3>
- The instantaneous rate of change from each of the four nucleotides to each of the other four nucleotides is summarized in the nucleotide substitution rate matrix.
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