This is a successive clustering method and is a term used to cover a multitude of different algorithms. Basically, the algorithm proceeds by assuming a 'star' topology
This a consensus tree formed from more than one fundamental tree. It only shows those clades that are in complete agreement in all of the fundamental trees. Also known as a strict component consensus tree.
Subtree Pruning Regrafting (SPR)
This is a heuristic search algorithm for searching through treespace. It proceeds by breaking off part of the tree and attaching it to another part of the tree. If it finds a better tree, then the new tree is used as a starting tree for another round of SPR. This is a more rigorous algorithm than NNI, but not as robust as TBR. Another name for SPR is cut-and-paste.
Alternatively known as Successive Approximation Character Weighting (SACW). This is a method of reweighting characters based on some measure of their relative values for the purposes of phylogeny reconstruction. If, for instance, an initial analysis is carried out and the result of this analysis indicates that some characters are quite inconsistent with the resulting tree(s), then these will be down-weighted in subsequent analyses. The index for downweighting the characters might be the retention index, consistency index or some such measure of consistency of a character with a tree. Iterative analyses are carried out, with the individual characters being reweighted each time until there is little or no change in the resulting topology.
Also known as multiple hits. These are substitutions that have occurred in one or more lineages subsequent to splitting. However, they are not seen in the contemporary taxa due to having been overlain by more recent changes.
These are characters that are shared by a number of sequences due to retention of the ancestral character state.
These are characters that are shared by a group of sequences due to recentness of common ancestry.
Those substitutions that do not change the identity of the encoded amino acid.
This is an umbrella term to describe the processes that describe species. There are three disciplines which are united under this broad locution. First there is the description of species (identification), then there is the naming of names (taxonomy) and then there is the description of the relationships among and between taxa (phylogenetics).
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