Glossary in Phylogeny Construction

T


Taxon (pl. taxa)

Also known as an operational taxonomic unit (OTU).  This is an individual, a strain, a species or any unit of classification.  In phylogeny reconstruction, the contemporary or hypothetical ancestral strain, species or whatever, is known as a taxon.  A hypothetical ancestor, a fossil and a clade are also known as taxa.

Taxonomy

This is the scientific discipline of naming organisms.  It was started by Carolus Linné (Carl Linneaus).   Taxonomy is one of the three branches of Systematics.

Transition

This is a substitution of a purine for a purine or a pyrimidine for a pyrimidine (like-for-like),

Transition Transversion Ratio

  1. This is a ratio of the number of transition to transversion substitutions that appear to have occurred since two sequences separated from a common ancestor. 
  2. This is the average rate of transition versus transversion substitutions in a dataset. 
  3. This is a value, estimated by reference to a tree that describes the average rate of transition to transversion during the evolutionary period covered by the tree.

Transversion

This is a substitution of a purine for a pyrimidine or vice versa.

Tree length

The sum of the estimated or actual branch lengths in tree.

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