Editing Phylogenetic tree (section)

== Construction ==
{{Main|Computational phylogenetics}}
Phylogenetic trees composed with a nontrivial number of input sequences are constructed using [[computational phylogenetics]] methods. Distance-matrix methods such as [[neighbor-joining]] or [[UPGMA]], which calculate [[genetic distance]] from [[multiple sequence alignment]]s, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as [[ClustalW]] also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. [[Maximum parsimony]] is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the [[optimality criterion]] of [[maximum likelihood]], often within a [[Bayesian inference|Bayesian framework]], and apply an explicit model of evolution to phylogenetic tree estimation.<ref name="Felsenstein" /> Identifying the optimal tree using many of these techniques is [[NP-hard]],<ref name="Felsenstein" /> so [[heuristic]] search and [[Optimization (mathematics)|optimization]] methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data.

Tree-building methods can be assessed on the basis of several criteria:<ref>{{cite journal | last1 = Penny | first1 = D. | last2 = Hendy | first2 = M. D. | last3 = Steel | first3 = M. A. | author3-link=Mike Steel (mathematician) | year = 1992 | title = Progress with methods for constructing evolutionary trees | journal = Trends in Ecology and Evolution | volume = 7 | issue = 3| pages = 73–79 | doi=10.1016/0169-5347(92)90244-6| pmid = 21235960 }}</ref>
* efficiency (how long does it take to compute the answer, how much memory does it need?)
* power (does it make good use of the data, or is information being wasted?)
* consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)
* robustness (does it cope well with violations of the assumptions of the underlying model?)
* falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)

Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using [[T-theory]].<ref>A. Dress, [[Katharina T. Huber|K. T. Huber]], and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. ''Documenta Mathematica'' ''LSU 2001'': 121–139</ref>

=== File formats ===
Trees can be encoded in a number of different formats, all of which must represent the nested structure of a tree. They may or may not encode branch lengths and other features. Standardized formats are critical for distributing and sharing trees without relying on graphics output that is hard to import into existing software. Commonly used formats are
* [[Nexus file|Nexus file format]] <ref name=":1">{{Cite web |title=Tree Formats |url=https://evomics.org/resources/tree-formats/ |access-date=2025-03-29 |website=Evolution and Genomics |language=en-US}}</ref>
* [[Newick format]] <ref name=":1" />