Distance-matrix Methods
Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance" between the sequences being classified, and therefore they require an MSA as an input. Distance is often defined as the fraction of mismatches at aligned positions, with gaps either ignored or counted as mismatches. Distance methods attempt to construct an all-to-all matrix from the sequence query set describing the distance between each sequence pair. From this is constructed a phylogenetic tree that places closely related sequences under the same interior node and whose branch lengths closely reproduce the observed distances between sequences. Distance-matrix methods may produce either rooted or unrooted trees, depending on the algorithm used to calculate them. They are frequently used as the basis for progressive and iterative types of multiple sequence alignments. The main disadvantage of distance-matrix methods is their inability to efficiently use information about local high-variation regions that appear across multiple subtrees.
Read more about this topic: Computational Phylogenetics
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