Editing Comparative genomics (section)

=== Phylogenetic reconstruction ===
Another computational method for comparative genomics is phylogenetic reconstruction. It is used to describe evolutionary relationships in terms of common ancestors. The relationships are usually represented in a tree called a [[phylogenetic tree]]. Similarly, [[coalescent theory]] is a retrospective model to trace alleles of a gene in a population to a single ancestral copy shared by members of the population. This is also known as the [[most recent common ancestor]]. Analysis based on coalescence theory tries predicting the amount of time between the introduction of a mutation and a particular allele or gene distribution in a population. This time period is equal to how long ago the most recent common ancestor existed. The inheritance relationships are visualized in a form similar to a phylogenetic tree. Coalescence (or the gene genealogy) can be visualized using [[dendrogram]]s.<ref>{{cite journal | vauthors = Haubold B, Wiehe T | title = Comparative genomics: methods and applications | journal = Die Naturwissenschaften | volume = 91 | issue = 9 | pages = 405–421 | date = September 2004 | pmid = 15278216 | doi = 10.1007/s00114-004-0542-8 | s2cid = 2041895 | bibcode = 2004NW.....91..405H }}</ref>
[[File:Synteny.png|thumb|upright=1.5|Example of synteny block and break. Genes located on chromosomes of two species are denoted in letters. Each gene is associated with a number representing the species they belong to (species 1 or 2). Orthologous genes are connected by dashed lines and genes without an orthologous relationship are treated as gaps in synteny programs.<ref>{{cite journal |vauthors=Liu D, Hunt M, Tsai IJ |title=Inferring synteny between genome assemblies: a systematic evaluation |journal=BMC Bioinformatics |volume=19 |issue=1 |pages=26 |date=January 2018 |pmid=29382321 |pmc=5791376 |doi=10.1186/s12859-018-2026-4 |doi-access=free}}</ref>]]