Editing Comparative genomics (section)

=== Whole-genome alignment ===
Whole-genome alignment (WGA) involves predicting evolutionary relationships at the nucleotide level between two or more genomes. It integrates elements of colinear sequence alignment and [[gene orthology]] prediction, presenting a greater challenge due to the vast size and intricate nature of whole genomes. Despite its complexity, numerous methods have emerged to tackle this problem because WGAs play a crucial role in various genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction.<ref>{{cite book | vauthors = Dewey CN | chapter = Whole-Genome Alignment | series = Methods in Molecular Biology | title = Evolutionary Genomics | volume = 855 | pages = 237–257 | date = 2012 | pmid = 22407711 | doi = 10.1007/978-1-61779-582-4_8 | publisher = Humana Press | isbn = 978-1-61779-581-7 | place = Totowa, NJ | veditors = Anisimova M }}</ref> Thereby, SyRI (Synteny and Rearrangement Identifier) is one such method that utilizes whole genome alignment and it is designed to identify both structural and sequence differences between two [[Sequence assembly|whole-genome assemblies]]. By taking WGAs as input, SyRI initially scans for disparities in genome structures. Subsequently, it identifies local sequence variations within both rearranged and non-rearranged (syntenic) regions.<ref>{{cite journal | doi=10.1186/s13059-019-1911-0 | doi-access=free | title=SyRI: Finding genomic rearrangements and local sequence differences from whole-genome assemblies | date=2019 | journal=Genome Biology | volume=20 | pmid=31842948 | vauthors = Goel M, Sun H, Jiao W, Schneeberger K | issue=1 | page=277 | pmc=6913012 }}</ref>

[[File:Betacoronavirus Phylogenetic Tree.png|thumb|upright=1.15 |Example of a phylogenetic tree created from an alignment of 250 unique spike protein sequences from the Betacoronavirus family.]]