There are two approaches, exhaustive and heuristic approaches, used in multiple sequence alignment. The exhaustive alignment method includes searching all possible aligned positions simultaneously. This…
Bayesian inference can be used to produce phylogenetic trees in a manner closely related to the maximum likelihood methods. Bayesian methods…
Maximum likelihood is the third method used to build trees. Likelihood provides probabilities of the sequences given a model of their evolution on a particular tree. The…
Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to…
Neighbor Joining Method (NJ) The neighbor joining (NJ) method can be used, which is somewhat similar to UPGMA in that…
UPGMA (unweighted pair group method with arithmetic mean) The UPGMA is the simplest distance-matrix method, and it employs sequential clustering to build a rooted phylogenetic…
Nucleotide bases fall into two categories depending on the ring structure of the base. Purines: A or G (these are two…
The statistical models used to correct homoplasy are called substitution models or evolutionary models. For constructing DNA phylogenies, there are…
Smith Waterman algorithm was first proposed by Temple F. Smith and Michael S. Waterman in 1981. The algorithm explains the…
Pairwise Algorithm A Pairwise Algorithm is an algorithmic technique with its origins in Dynamic programming. Pairwise algorithms have many uses including comparing a protein profile…