Editing Phylogenetic tree (section)

=== Rooted tree ===
[[File:Phylogenetic treePureThickBraille.jpg|thumb|upright=1.35 |Rooted phylogenetic tree optimized for blind people. The lowest point of the tree is the root, which symbolizes the universal common ancestor to all living beings. The tree branches out into three main groups: Bacteria (left branch, letters a to i), Archea (middle branch, letters j to p) and Eukaryota (right branch, letters q to z). Each letter corresponds to a group of organisms, listed below this description. These letters and the description should be converted to Braille font, and printed using a Braille printer. The figure can be 3D printed by copying the png file and using Cura or other software to generate the Gcode for 3D printing.]]
A rooted phylogenetic [[Tree (data structure)|tree]] (see two graphics at top) is a [[directed graph|directed]] tree with a unique node — the root — corresponding to the (usually [[imputation (statistics)|imputed]]) most recent common ancestor of all the entities at the [[leaf node|leaves]] of the tree. The root node does not have a parent node, but serves as the parent of all other nodes in the tree. The root is therefore a node of [[Node (computer science)#Nodes and trees|degree]] 2, while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges).{{cn|date=June 2024}}

The most common method for rooting trees is the use of an uncontroversial [[outgroup (cladistics)|outgroup]]—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup. Another method is midpoint rooting, or a tree can also be rooted by using a non-stationary [[substitution model]].<ref>{{cite journal |last1=Dang |first1=Cuong Cao |last2=Minh |first2=Bui Quang |last3=McShea |first3=Hanon |last4=Masel |first4=Joanna |last5=James |first5=Jennifer Eleanor |last6=Vinh |first6=Le Sy |last7=Lanfear |first7=Robert |title=nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models |journal=Systematic Biology |date=9 February 2022 |volume=71 |issue=5 |pages=1110–1123 |doi=10.1093/sysbio/syac007|pmid=35139203 |pmc=9366462 }}</ref>