Genomes change overtime. There are mutations, deletions, insertions, and other rearangements that can change the genes and genome of an organism. When we reconstruct the phylogeny of a group of organisms, we must first create an alignment where each column, site, corresponds in each tip. This must be done because each phylogenetic method conducts per site reonstruction.

In this chapter we discuss a few of the most common methods for alignment creation. This gives a basic overview, however there are many methods to practically carry out alignment estimation.

Sections

1. Scoring Matrices
2. Global Alignment
3. Local Alignment