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<p>A <strong>phylogenetic tree</strong> or <strong>evolutionary tree</strong> is a branching <a href="https://en.wikipedia.org/wiki/Diagram" title="Diagram">diagram</a> or "<a href="https://en.wikipedia.org/wiki/Tree_(graph_theory)" title="Tree (graph theory)">tree</a>" showing the <a href="https://en.wikipedia.org/wiki/Evolution" title="Evolution">evolutionary</a> relationships among various biological <a href="https://en.wikipedia.org/wiki/Species" title="Species">species</a> or other entities—their <strong>phylogeny</strong> (<a href="https://en.wikipedia.org/wiki/Help:IPA/English" title="Help:IPA/English">/faɪˈlɒdʒəni/</a>)—based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating <a href="https://en.wikipedia.org/wiki/Common_ancestry" title="Common ancestry">common ancestry</a>.</p>
<p>In a <em>rooted</em> phylogenetic tree, each node with descendants represents the inferred <a href="https://en.wikipedia.org/wiki/Most_recent_common_ancestor" title="Most recent common ancestor">most recent common ancestor</a> of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as <a href="https://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a>, <a href="https://en.wikipedia.org/wiki/Systematics" title="Systematics">systematics</a>, and <a href="https://en.wikipedia.org/wiki/Phylogenetics" title="Phylogenetics">phylogenetics</a>. <em>Unrooted</em> trees illustrate only the relatedness of the <a href="https://en.wikipedia.org/wiki/Leaf_nodes" title="Leaf nodes">leaf nodes</a> and do not require the ancestral root to be known or inferred.</p>
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<h2>Contents</h2>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#History">1History</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Types">2Types</a>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Rooted_tree">2.1Rooted tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Unrooted_tree">2.2Unrooted tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Bifurcating_tree">2.3Bifurcating tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Special_tree_types">2.4Special tree types</a></li>
</ul>
</li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Construction">3Construction</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Limitations">4Limitations</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#See_also">5See also</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#References">6References</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Further_reading">7Further reading</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#External_links">8External links</a>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Images">8.1Images</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#General">8.2General</a></li>
</ul>
</li>
</ul>
<h2>History[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=1" title="Edit section: History">edit</a>]</h2>
<p>The idea of a "<a href="https://en.wikipedia.org/wiki/Tree_of_life_(science)" title="Tree of life (science)">tree of life</a>" arose from ancient notions of a ladder-like progression from lower into higher forms of <a href="https://en.wikipedia.org/wiki/Life" title="Life">life</a> (such as in the <a href="https://en.wikipedia.org/wiki/Great_Chain_of_Being" title="Great Chain of Being">Great Chain of Being</a>). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book <em>Elementary Geology</em>, by Edward Hitchcock (first edition: 1840).</p>
<p><a href="https://en.wikipedia.org/wiki/Charles_Darwin" title="Charles Darwin">Charles Darwin</a> (1859) also produced one of the first illustrations and crucially popularized the notion of an <a href="https://en.wikipedia.org/wiki/Natural_selection" title="Natural selection">evolutionary "tree"</a>in his seminal book <em><a href="https://en.wikipedia.org/wiki/The_Origin_of_Species" title="The Origin of Species">The Origin of Species</a></em>. Over a century later, <a href="https://en.wikipedia.org/wiki/Evolutionary_biology" title="Evolutionary biology">evolutionary biologists</a> still use <a href="https://en.wikipedia.org/wiki/Tree_structure" title="Tree structure">tree diagrams</a> to depict <a href="https://en.wikipedia.org/wiki/Evolution" title="Evolution">evolution</a> because such diagrams effectively convey the concept that <a href="https://en.wikipedia.org/wiki/Speciation" title="Speciation">speciation</a> occurs through the <a href="https://en.wikipedia.org/wiki/Adaptation" title="Adaptation">adaptive</a> and semi<a href="https://en.wikipedia.org/wiki/Random" title="Random">random</a>splitting of lineages. Over time, species classification has become less static and more dynamic.</p>
<p>The term <em>phylogenetic</em>, or <em>phylogeny</em>, derives from the two <a href="https://en.wikipedia.org/wiki/Ancient_greek" title="Ancient greek">ancient greek</a> words <a href="https://en.wiktionary.org/wiki/%CF%86%E1%BF%A6%CE%BB%CE%BF%CE%BD#Ancient_Greek" title="wikt:φῦλον">φῦλον</a> (<em>phûlon</em>), meaning "race, lineage", and <a href="https://en.wiktionary.org/wiki/%CE%B3%CE%AD%CE%BD%CE%B5%CF%83%CE%B9%CF%82#Ancient_Greek" title="wikt:γένεσις">γένεσις</a> (<em>génesis</em>), meaning "origin, source".<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-1">[1]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-2">[2]</a></sup></p>
<h2>Types[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=2" title="Edit section: Types">edit</a>]</h2>
<h3>Rooted tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=3" title="Edit section: Rooted tree">edit</a>]</h3>
<p>A rooted phylogenetic tree (see two graphics at top) is a <a href="https://en.wikipedia.org/wiki/Directed_graph" title="Directed graph">directed</a> <a href="https://en.wikipedia.org/wiki/Tree_(data_structure)" title="Tree (data structure)">tree</a> with a unique node — the root — corresponding to the (usually <a href="https://en.wikipedia.org/wiki/Imputation_(statistics)" title="Imputation (statistics)">imputed</a>) most recent common ancestor of all the entities at the <a href="https://en.wikipedia.org/wiki/Leaf_node" title="Leaf node">leaves</a> 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 <a href="https://en.wikipedia.org/wiki/Node_(computer_science)#Nodes_and_trees" title="Node (computer science)">degree</a> 2 while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges).</p>
<p>The most common method for rooting trees is the use of an uncontroversial <a href="https://en.wikipedia.org/wiki/Outgroup_(cladistics)" title="Outgroup (cladistics)">outgroup</a>—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.</p>
<h3>Unrooted tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=4" title="Edit section: Unrooted tree">edit</a>]</h3>
<p><a href="https://en.wikipedia.org/wiki/File:MyosinUnrootedTree.jpg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/MyosinUnrootedTree.jpg/340px-MyosinUnrootedTree.jpg" style="height:240px; width:340px" /></a></p>
<p>An unrooted phylogenetic tree for <a href="https://en.wikipedia.org/wiki/Myosin" title="Myosin">myosin</a>, a <a href="https://en.wikipedia.org/wiki/Gene_family" title="Gene family">superfamily</a> of <a href="https://en.wikipedia.org/wiki/Protein" title="Protein">proteins</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Hodge_2000-3">[3]</a></sup></p>
<p>Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-4">[4]</a></sup> Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the <a href="https://en.wikipedia.org/wiki/Molecular_clock" title="Molecular clock">molecular clock</a> <a href="https://en.wikipedia.org/wiki/Hypothesis" title="Hypothesis">hypothesis</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Maher_2002-5">[5]</a></sup></p>
<h3>Bifurcating tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=5" title="Edit section: Bifurcating tree">edit</a>]</h3>
<p>Both rooted and unrooted phylogenetic trees can be either <a href="https://en.wikipedia.org/wiki/Bifurcation_theory" title="Bifurcation theory">bifurcating</a> or multifurcating, and either labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each <a href="https://en.wikipedia.org/wiki/Interior_node" title="Interior node">interior node</a> (that is, it forms a <a href="https://en.wikipedia.org/wiki/Binary_tree" title="Binary tree">binary tree</a>), and an unrooted bifurcating tree takes the form of an <a href="https://en.wikipedia.org/wiki/Unrooted_binary_tree" title="Unrooted binary tree">unrooted binary tree</a>, a <a href="https://en.wikipedia.org/wiki/Free_tree" title="Free tree">free tree</a> with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For labeled bifurcating trees, there are:</p>
<p>{\displaystyle (2n-3)!!={\frac {(2n-3)!}{2^{n-2}(n-2)!}}\,\,{\text{for}}\,n\geq 2}<img alt="{\displaystyle (2n-3)!!={\frac {(2n-3)!}{2^{n-2}(n-2)!}}\,\,{\text{for}}\,n\geq 2}" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/cc3ce2c88666896f262dde1714ecdf2fbf160d47" /></p>
<p>total rooted trees and</p>
<p>{\displaystyle (2n-5)!!={\frac {(2n-5)!}{2^{n-3}(n-3)!}}\,\,{\text{for}}\,n\geq 3}<img alt="{\displaystyle (2n-5)!!={\frac {(2n-5)!}{2^{n-3}(n-3)!}}\,\,{\text{for}}\,n\geq 3}" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/2d595b11feed87c05ed569f80a141e712d1105c7" /></p>
<p>total unrooted trees, where {\displaystyle n}<img alt="n" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/a601995d55609f2d9f5e233e36fbe9ea26011b3b" /> represents the number of leaf nodes. Among labeled bifurcating trees, the number of unrooted trees with {\displaystyle n}<img alt="n" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/a601995d55609f2d9f5e233e36fbe9ea26011b3b" /> leaves is equal to the number of rooted trees with {\displaystyle n-1}<img alt="n-1" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/fbd0b0f32b28f51962943ee9ede4fb34198a2521" />leaves.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup></p>
<h3>Special tree types[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=6" title="Edit section: Special tree types">edit</a>]</h3>
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<p>This section <strong>does not <a href="https://en.wikipedia.org/wiki/Wikipedia:Citing_sources" title="Wikipedia:Citing sources">cite</a> any <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability">sources</a></strong>. Please help <a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit">improve this section</a> by <a href="https://en.wikipedia.org/wiki/Help:Introduction_to_referencing_with_Wiki_Markup/1" title="Help:Introduction to referencing with Wiki Markup/1">adding citations to reliable sources</a>. Unsourced material may be challenged and <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability#Burden_of_evidence" title="Wikipedia:Verifiability">removed</a>. <small><em>(October 2012)</em></small><small><em> (<a href="https://en.wikipedia.org/wiki/Help:Maintenance_template_removal" title="Help:Maintenance template removal">Learn how and when to remove this template message</a>)</em></small></p>
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<p><a href="https://en.wikipedia.org/wiki/File:Spindle_diagram.jpg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/7/76/Spindle_diagram.jpg/220px-Spindle_diagram.jpg" style="height:153px; width:220px" /></a></p>
<p>A spindle diagram, showing the evolution of the <a href="https://en.wikipedia.org/wiki/Vertebrate" title="Vertebrate">vertebrates</a> at class level, width of spindles indicating number of families. Spindle diagrams are often used in <a href="https://en.wikipedia.org/wiki/Evolutionary_taxonomy" title="Evolutionary taxonomy">evolutionary taxonomy</a>.</p>
<p><a href="https://en.wikipedia.org/wiki/File:Tree_of_life_SVG.svg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/340px-Tree_of_life_SVG.svg.png" style="height:340px; width:340px" /></a></p>
<p>A highly resolved, automatically generated <a href="https://en.wikipedia.org/wiki/Tree_of_life_(biology)" title="Tree of life (biology)">tree of life</a>, based on completely sequenced genomes.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-7">[7]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-8">[8]</a></sup></p>
<ul>
<li>A <a href="https://en.wikipedia.org/wiki/Dendrogram" title="Dendrogram">dendrogram</a> is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-9">[9]</a></sup></li>
<li>A <a href="https://en.wikipedia.org/wiki/Cladogram" title="Cladogram">cladogram</a> is a phylogenetic tree formed using <a href="https://en.wikipedia.org/wiki/Cladistics" title="Cladistics">cladistic</a> methods. This type of tree only represents a branching pattern; i.e., its branch spans do not represent time or relative amount of character change.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-10">[10]</a></sup></li>
<li>A phylogram is a phylogenetic tree that has branch spans proportional to the amount of character change.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-11">[11]</a></sup></li>
<li>A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch spans.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Santamaria2009-12">[12]</a></sup></li>
<li>A spindle diagram (often called a Romerogram after the American palaeontologist <a href="https://en.wikipedia.org/wiki/Alfred_Romer" title="Alfred Romer">Alfred Romer</a>) is the representation of the evolution and abundance of the various taxa through time.</li>
<li>A <a href="https://en.wikipedia.org/wiki/Rolf_Dahlgren" title="Rolf Dahlgren">Dahlgrenogram</a> is a diagram representing a cross section of a phylogenetic tree</li>
<li>A <a href="https://en.wikipedia.org/wiki/Phylogenetic_network" title="Phylogenetic network">phylogenetic network</a> is not strictly speaking a tree, but rather a more general <a href="https://en.wikipedia.org/wiki/Graph_(discrete_mathematics)" title="Graph (discrete mathematics)">graph</a>, or a <a href="https://en.wikipedia.org/wiki/Directed_acyclic_graph" title="Directed acyclic graph">directed acyclic graph</a> in the case of rooted networks. They are used to overcome some of the <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Limitations" title="Phylogenetic tree">limitations</a> inherent to trees.</li>
</ul>
<h2>Construction[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=7" title="Edit section: Construction">edit</a>]</h2>
<p>Main article: <a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">Computational phylogenetics</a></p>
<p>Phylogenetic trees composed with a nontrivial number of input sequences are constructed using <a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">computational phylogenetics</a> methods. Distance-matrix methods such as <a href="https://en.wikipedia.org/wiki/Neighbor-joining" title="Neighbor-joining">neighbor-joining</a> or <a href="https://en.wikipedia.org/wiki/UPGMA" title="UPGMA">UPGMA</a>, which calculate <a href="https://en.wikipedia.org/wiki/Genetic_distance" title="Genetic distance">genetic distance</a> from <a href="https://en.wikipedia.org/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">multiple sequence alignments</a>, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as <a href="https://en.wikipedia.org/wiki/ClustalW" title="ClustalW">ClustalW</a> also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. <a href="https://en.wikipedia.org/wiki/Maximum_parsimony" title="Maximum parsimony">Maximum parsimony</a> is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the <a href="https://en.wikipedia.org/wiki/Optimality_criterion" title="Optimality criterion">optimality criterion</a> of <a href="https://en.wikipedia.org/wiki/Maximum_likelihood" title="Maximum likelihood">maximum likelihood</a>, often within a <a href="https://en.wikipedia.org/wiki/Bayesian_inference" title="Bayesian inference">Bayesian Framework</a>, and apply an explicit model of evolution to phylogenetic tree estimation.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup> Identifying the optimal tree using many of these techniques is <a href="https://en.wikipedia.org/wiki/NP-hard" title="NP-hard">NP-hard</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup> so <a href="https://en.wikipedia.org/wiki/Heuristic" title="Heuristic">heuristic</a> search and <a href="https://en.wikipedia.org/wiki/Optimization_(mathematics)" title="Optimization (mathematics)">optimization</a> methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data.</p>
<p>Tree-building methods can be assessed on the basis of several criteria:<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-13">[13]</a></sup></p>
<ul>
<li>efficiency (how long does it take to compute the answer, how much memory does it need?)</li>
<li>power (does it make good use of the data, or is information being wasted?)</li>
<li>consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)</li>
<li>robustness (does it cope well with violations of the assumptions of the underlying model?)</li>
<li>falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)</li>
</ul>
<p>Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using <a href="https://en.wikipedia.org/wiki/T-theory" title="T-theory">T-theory</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-14">[14]</a></sup></p>
<h2>Limitations[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=8" title="Edit section: Limitations">edit</a>]</h2>
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<p>This section <strong>needs additional citations for <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability">verification</a></strong>. Please help <a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit">improve this article</a> by <a href="https://en.wikipedia.org/wiki/Help:Introduction_to_referencing_with_Wiki_Markup/1" title="Help:Introduction to referencing with Wiki Markup/1">adding citations to reliable sources</a>. Unsourced material may be challenged and removed. <small><em>(October 2012)</em></small><small><em> (<a href="https://en.wikipedia.org/wiki/Help:Maintenance_template_removal" title="Help:Maintenance template removal">Learn how and when to remove this template message</a>)</em></small></p>
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<p>Although phylogenetic trees produced on the basis of sequenced <a href="https://en.wikipedia.org/wiki/Gene" title="Gene">genes</a> or <a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genomic</a> data in different species can provide evolutionary insight, they have important limitations. Most importantly, they do not necessarily accurately represent the evolutionary history of the included taxa. In fact, they are literally scientific <a href="https://en.wikipedia.org/wiki/Hypotheses" title="Hypotheses">hypotheses</a>, subject to <a href="https://en.wikipedia.org/wiki/Falsifiability" title="Falsifiability">falsification</a> by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based is <a href="https://en.wikipedia.org/wiki/Signal_noise" title="Signal noise">noisy</a>;<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Townsend_2012-15">[15]</a></sup> the analysis can be confounded by <a href="https://en.wikipedia.org/wiki/Genetic_recombination" title="Genetic recombination">genetic recombination</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Arenas_2010-16">[16]</a></sup> <a href="https://en.wikipedia.org/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">horizontal gene transfer</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Woese_2002-17">[17]</a></sup><a href="https://en.wikipedia.org/wiki/Hybrid_(biology)" title="Hybrid (biology)">hybridisation</a> between species that were not nearest neighbors on the tree before hybridisation takes place, <a href="https://en.wikipedia.org/wiki/Convergent_evolution" title="Convergent evolution">convergent evolution</a>, and <a href="https://en.wikipedia.org/wiki/Conserved_sequence" title="Conserved sequence">conserved sequences</a>.</p>
<p>Also, there are problems in basing the analysis on a single type of character, such as a single <a href="https://en.wikipedia.org/wiki/Gene" title="Gene">gene</a> or <a href="https://en.wikipedia.org/wiki/Protein" title="Protein">protein</a> or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This is most true of genetic material that is subject to lateral gene transfer and <a href="https://en.wikipedia.org/wiki/Genetic_recombination" title="Genetic recombination">recombination</a>, where different <a href="https://en.wikipedia.org/wiki/Haplotype" title="Haplotype">haplotype</a> blocks can have different histories. In general, the output tree of a phylogenetic analysis is an estimate of the <em>character'</em>s phylogeny (i.e. a gene tree) and not the phylogeny of the <a href="https://en.wikipedia.org/wiki/Taxa" title="Taxa">taxa</a> (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use a combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be expected to evolve under different selective regimes, so that <a href="https://en.wikipedia.org/wiki/Homoplasy" title="Homoplasy">homoplasy</a> (false <a href="https://en.wikipedia.org/wiki/Homology_(biology)" title="Homology (biology)">homology</a>) would be unlikely to result from natural selection.</p>
<p>When extinct species are included in a tree, they are <a href="https://en.wikipedia.org/wiki/Leaf_node" title="Leaf node">terminal nodes</a>, as it is unlikely that they are direct ancestors of any extant species. Skepticism might be applied when extinct species are included in trees that are wholly or partly based on DNA sequence data, because little useful "<a href="https://en.wikipedia.org/wiki/Ancient_DNA" title="Ancient DNA">ancient DNA</a>" is preserved for longer than 100,000 years, and except in the most unusual circumstances no DNA sequences long enough for use in phylogenetic analyses have yet been recovered from material over 1 million years old.<sup>[<em><a href="https://en.wikipedia.org/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed">citation needed</a></em>]</sup></p>
<p>The range of useful DNA materials has expanded with advances in extraction and sequencing technologies. Development of technologies able to infer sequences from smaller fragments, or from spatial patterns of DNA degradation products, would further expand the range of DNA considered useful.</p>
<p>In some organisms, <a href="https://en.wikipedia.org/wiki/Endosymbiont" title="Endosymbiont">endosymbionts</a> have an independent genetic history from the host.</p>
<p><a href="https://en.wikipedia.org/wiki/Phylogenetic_network" title="Phylogenetic network">Phylogenetic networks</a> are used when bifurcating trees are not suitable, due to these complications which suggest a more <a href="https://en.wikipedia.org/wiki/Reticulate" title="Reticulate">reticulate</a> evolutionary history of the organisms sampled.</p>
<h2>See also[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=9" title="Edit section: See also">edit</a>]</h2>
<ul>
<li><a href="https://en.wikipedia.org/wiki/File:Tree_of_life.svg"><img alt="icon" src="https://upload.wikimedia.org/wikipedia/commons/thumb/0/09/Tree_of_life.svg/32px-Tree_of_life.svg.png" style="height:27px; width:32px" /></a><a href="https://en.wikipedia.org/wiki/Portal:Evolutionary_biology" title="Portal:Evolutionary biology">Evolutionary biology portal</a></li>
</ul>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Cladistics" title="Cladistics">Cladistics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Comparative_phylogenetics" title="Comparative phylogenetics">Comparative phylogenetics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">Computational phylogenetics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Evolutionary_taxonomy" title="Evolutionary taxonomy">Evolutionary taxonomy</a></li>
<li><a href="https://en.wikipedia.org/wiki/Evolutionary_biology" title="Evolutionary biology">Evolutionary biology</a></li>
<li><a href="https://en.wikipedia.org/wiki/Generalized_tree_alignment" title="Generalized tree alignment">Generalized tree alignment</a></li>
<li><a href="https://en.wikipedia.org/wiki/List_of_phylogenetics_software" title="List of phylogenetics software">List of phylogenetics software</a></li>
<li><a href="https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software" title="List of phylogenetic tree visualization software">List of phylogenetic tree visualization software</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_comparative_methods" title="Phylogenetic comparative methods">Phylogenetic comparative methods</a></li>
</ul>
<h2>References[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=10" title="Edit section: References">edit</a>]</h2>
<ol>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-1" title="Jump up">^</a></strong> <cite>Bailly, Anatole (1981-01-01). <a href="https://www.worldcat.org/oclc/461974285" rel="nofollow"><em>Abrégé du dictionnaire grec français</em></a>. Paris: Hachette. <a href="https://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number">ISBN</a> <a href="https://en.wikipedia.org/wiki/Special:BookSources/978-2010035289" title="Special:BookSources/978-2010035289">978-2010035289</a>. <a href="https://en.wikipedia.org/wiki/OCLC" title="OCLC">OCLC</a> <a href="https://www.worldcat.org/oclc/461974285" rel="nofollow">461974285</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-2" title="Jump up">^</a></strong> <cite>Bailly, Anatole. <a href="http://www.tabularium.be/bailly/" rel="nofollow">"Greek-french dictionary online"</a>. <em>www.tabularium.be</em>. <a href="https://web.archive.org/web/20140421003247/http://www.tabularium.be/bailly/" rel="nofollow">Archived</a> from the original on April 21, 2014. Retrieved March 2, 2018.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Hodge_2000_3-0" title="Jump up">^</a></strong> <cite>Hodge T, Cope M (1 October 2000). <a href="http://jcs.biologists.org/cgi/content/full/113/19/3353" rel="nofollow">"A myosin family tree"</a>. <em>J Cell Sci</em>. <strong>113</strong> (19): 3353–4. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/10984423" rel="nofollow">10984423</a>. <a href="https://web.archive.org/web/20070930043742/http://jcs.biologists.org/cgi/content/full/113/19/3353" rel="nofollow">Archived</a> from the original on 30 September 2007.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-4" title="Jump up">^</a></strong> <cite><a href="https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html" rel="nofollow">"Archived copy"</a>. <a href="https://web.archive.org/web/20140414030413/http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html" rel="nofollow">Archived</a> from the original on 2014-04-14. Retrieved 2014-05-26.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Maher_2002_5-0" title="Jump up">^</a></strong> <cite>Maher BA (2002). <a href="http://www.the-scientist.com/yr2002/sep/research1_020916.html" rel="nofollow">"Uprooting the Tree of Life"</a>. <em>The Scientist</em>. <strong>16</strong>: 18. <a href="https://web.archive.org/web/20031002231607/http://www.the-scientist.com/yr2002/sep/research1_020916.html" rel="nofollow">Archived</a> from the original on 2003-10-02.</cite></li>
<li>^ <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-0">Jump up to:<sup><em><strong>a</strong></em></sup></a> <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-1"><sup><em><strong>b</strong></em></sup></a> <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-2"><sup><em><strong>c</strong></em></sup></a> Felsenstein J. (2004). <em>Inferring Phylogenies</em> Sinauer Associates: Sunderland, MA.</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-7" title="Jump up">^</a></strong> <cite>Letunic, Ivica; <a href="https://en.wikipedia.org/wiki/Peer_Bork" title="Peer Bork">Bork, Peer</a> (1 January 2007). <a href="http://itol.embl.de/help/17050570.pdf" rel="nofollow">"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation"</a> (PDF). <em><a href="https://en.wikipedia.org/wiki/Bioinformatics_(journal)" title="Bioinformatics (journal)">Bioinformatics</a></em>. Cambridge. <strong>23</strong> (1): 127–128. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtl529" rel="nofollow">10.1093/bioinformatics/btl529</a>. <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number" title="International Standard Serial Number">ISSN</a> <a href="https://www.worldcat.org/issn/1367-4803" rel="nofollow">1367-4803</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/17050570" rel="nofollow">17050570</a>. <a href="https://web.archive.org/web/20151129010406/http://itol.embl.de/help/17050570.pdf" rel="nofollow">Archived</a> (PDF) from the original on November 29, 2015. Retrieved 2015-07-21.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-8" title="Jump up">^</a></strong> <cite>Ciccarelli, FD; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006). <a href="http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf" rel="nofollow">"Toward automatic reconstruction of a highly resolved tree of life"</a> (Submitted manuscript). <em>Science</em>. <strong>311</strong>(5765): 1283–7. <a href="https://en.wikipedia.org/wiki/Bibcode" title="Bibcode">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2006Sci...311.1283C" rel="nofollow">2006Sci...311.1283C</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1126%2Fscience.1123061" rel="nofollow">10.1126/science.1123061</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/16513982" rel="nofollow">16513982</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-9" title="Jump up">^</a></strong> <cite>Fox, Emily. <a href="https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram" rel="nofollow">"The dendrogram"</a>. <em>coursea</em>. coursea. <a href="https://web.archive.org/web/20170928060157/https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram" rel="nofollow">Archived</a>from the original on 28 September 2017. Retrieved 28 September2017.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-10" title="Jump up">^</a></strong> Mayr, Ernst (2009)"Cladistic analysis or cladistic classification?". Journal of Zoological Systematics and Evolutionary Research. 12: 94–128. doi:10.1111/j.1439-0469.1974.tb00160.x..</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-11" title="Jump up">^</a></strong> Antonio Soares, Ricardo Râbelo, Alexandre Delbem, Optimization based on phylogram analysis, In Expert Systems with Applications, Volume 78, 2017, Pages 32-50, ISSN 0957-4174, <a href="https://doi.org/10.1016/j.eswa.2017.02.012" rel="nofollow">https://doi.org/10.1016/j.eswa.2017.02.012</a>.</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Santamaria2009_12-0" title="Jump up">^</a></strong> <cite>Santamaria, R.; Theron, R. (2009-05-26). <a href="https://academic.oup.com/bioinformatics/article/25/15/1970/212219" rel="nofollow">"Treevolution: visual analysis of phylogenetic trees"</a>. <em>Bioinformatics</em>. <strong>25</strong> (15): 1970–1971. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtp333" rel="nofollow">10.1093/bioinformatics/btp333</a>. <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number" title="International Standard Serial Number">ISSN</a> <a href="https://www.worldcat.org/issn/1367-4803" rel="nofollow">1367-4803</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-13" title="Jump up">^</a></strong> <cite>Penny, D.; Hendy, M. D.; <a href="https://en.wikipedia.org/wiki/Mike_Steel_(mathematician)" title="Mike Steel (mathematician)">Steel, M. A.</a> (1992). "Progress with methods for constructing evolutionary trees". <em>Trends in Ecology and Evolution</em>. <strong>7</strong> (3): 73–79. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1016%2F0169-5347%2892%2990244-6" rel="nofollow">10.1016/0169-5347(92)90244-6</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/21235960" rel="nofollow">21235960</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-14" title="Jump up">^</a></strong> A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. <em>Documenta Mathematica</em> <em>LSU 2001</em>: 121-139</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Townsend_2012_15-0" title="Jump up">^</a></strong> <cite>Townsend JP, Su Z, Tekle Y (2012). "Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny". <em>Genetics</em>. <strong>61</strong> (5): 835–849. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fsysbio%2Fsys036" rel="nofollow">10.1093/sysbio/sys036</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/22389443" rel="nofollow">22389443</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Arenas_2010_16-0" title="Jump up">^</a></strong> <cite>Arenas M, Posada D (2010). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865913" rel="nofollow">"The effect of recombination on the reconstruction of ancestral sequences"</a>. <em>Genetics</em>. <strong>184</strong> (4): 1133–1139. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1534%2Fgenetics.109.113423" rel="nofollow">10.1534/genetics.109.113423</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865913" rel="nofollow">2865913</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/20124027" rel="nofollow">20124027</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Woese_2002_17-0" title="Jump up">^</a></strong> <cite>Woese C (2002). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369" rel="nofollow">"On the evolution of cells"</a>. <em>Proc Natl Acad Sci USA</em>. <strong>99</strong> (13): 8742–7. <a href="https://en.wikipedia.org/wiki/Bibcode" title="Bibcode">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2002PNAS...99.8742W" rel="nofollow">2002PNAS...99.8742W</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1073%2Fpnas.132266999" rel="nofollow">10.1073/pnas.132266999</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369" rel="nofollow">124369</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/12077305" rel="nofollow">12077305</a>.</cite></li>
</ol>
<h2>Further reading[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=11" title="Edit section: Further reading">edit</a>]</h2>
<ul>
<li>Schuh, R. T. and A. V. Z. Brower. 2009. <em>Biological Systematics: principles and applications (2nd edn.)</em> <a href="https://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number">ISBN</a> <a href="https://en.wikipedia.org/wiki/Special:BookSources/978-0-8014-4799-0" title="Special:BookSources/978-0-8014-4799-0">978-0-8014-4799-0</a></li>
<li><a href="https://en.wikipedia.org/wiki/Manuel_Lima" title="Manuel Lima">Manuel Lima</a>, <em>The Book of Trees: Visualizing Branches of Knowledge</em>, 2014, Princeton Architectural Press, New York.</li>
<li><a href="https://en.wikipedia.org/wiki/MEGA,_Molecular_Evolutionary_Genetics_Analysis" title="MEGA, Molecular Evolutionary Genetics Analysis">MEGA</a>, a free software to draw phylogenetic trees.</li>
</ul>
<h2>External links[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=12" title="Edit section: External links">edit</a>]</h2>
<table>
<tbody>
<tr>
<td><img alt="" src="https://upload.wikimedia.org/wikipedia/en/thumb/4/4a/Commons-logo.svg/30px-Commons-logo.svg.png" style="height:40px; width:30px" /></td>
<td>Wikimedia Commons has media related to <em><strong><a href="https://commons.wikimedia.org/wiki/Category:Phylogenetic_tree_of_life" title="commons:Category:Phylogenetic tree of life">Phylogenetic tree</a></strong></em>.</td>
</tr>
</tbody>
</table>
<h3>Images[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=13" title="Edit section: Images">edit</a>]</h3>
<ul>
<li><a href="https://www.webcitation.org/66QTvQVdZ?url=http://ycc.biosci.arizona.edu/nomenclature_system/fig1.html" rel="nofollow">Human Y-Chromosome 2002 Phylogenetic Tree</a></li>
<li><a href="http://itol.embl.de/" rel="nofollow">iTOL: Interactive Tree Of Life</a></li>
<li><a href="http://picbreeder.com/tol.php" rel="nofollow">Phylogenetic Tree of Artificial Organisms Evolved on Computers</a></li>
<li><a href="https://web.archive.org/web/20110210200039/http://phylogram.org/" rel="nofollow">Miyamoto and Goodman's Phylogram of Eutherian Mammals</a></li>
</ul>
<h3>General[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=14" title="Edit section: General">edit</a>]</h3>
<ul>
<li>An overview of different methods of tree visualization is available at <cite>Page, R. D. M. (2011). "Space, time, form: Viewing the Tree of Life". <em>Trends in Ecology & Evolution</em>. <strong>27</strong> (2): 113–120. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1016%2Fj.tree.2011.12.002" rel="nofollow">10.1016/j.tree.2011.12.002</a>.</cite></li>
<li><a href="http://www.discoverlife.org/tree" rel="nofollow">Discover Life</a> An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project</li>
<li><a href="https://web.archive.org/web/20071114093618/http://www.ohiou.edu/phylocode/index.html" rel="nofollow">PhyloCode</a></li>
<li><a href="http://webarchive.loc.gov/all/20011109204837/http://www.mrc-lmb.cam.ac.uk/myosin/trees/trees.html" rel="nofollow">A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree</a></li>
<li><a href="http://tolweb.org/tree" rel="nofollow">Tree of Life Web Project</a></li>
<li><a href="http://www.trex.uqam.ca/" rel="nofollow">Phylogenetic inferring on the T-REX server</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/" rel="nofollow">NCBI's Taxonomy Database</a><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/" rel="nofollow">[1]</a></li>
<li><a href="https://web.archive.org/web/20140525220921/http://ete.cgenomics.org/" rel="nofollow">ETE: A Python Environment for Tree Exploration</a> This is a programming library to analyze, manipulate and visualize phylogenetic trees. <a href="http://www.biomedcentral.com/1471-2105/11/24" rel="nofollow">Ref.</a></li>
<li><a href="http://supfam.org/SUPERFAMILY/sTOL" rel="nofollow">A daily-updated tree of (sequenced) life</a> <cite>Fang, H.; Oates, M. E.; Pethica, R. B.; Greenwood, J. M.; Sardar, A. J.; Rackham, O. J. L.; Donoghue, P. C. J.; Stamatakis, A.; De Lima Morais, D. A.; Gough, J. (2013). "A daily-updated tree of (sequenced) life as a reference for genome research". <em>Scientific Reports</em>. <strong>3</strong>: 2015. <a href="https://en.wikipedia.org/wiki/Bibcode" title="">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2013NatSR...3E2015F" rel="nofollow">2013NatSR...3E2015F</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1038%2Fsrep02015" rel="nofollow">10.1038/srep02015</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/23778980" rel="nofollow">23778980</a>.</cite></li>
</ul>
<p>In a <em>rooted</em> phylogenetic tree, each node with descendants represents the inferred <a href="https://en.wikipedia.org/wiki/Most_recent_common_ancestor" title="Most recent common ancestor">most recent common ancestor</a> of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as <a href="https://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a>, <a href="https://en.wikipedia.org/wiki/Systematics" title="Systematics">systematics</a>, and <a href="https://en.wikipedia.org/wiki/Phylogenetics" title="Phylogenetics">phylogenetics</a>. <em>Unrooted</em> trees illustrate only the relatedness of the <a href="https://en.wikipedia.org/wiki/Leaf_nodes" title="Leaf nodes">leaf nodes</a> and do not require the ancestral root to be known or inferred.</p>
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<h2>Contents</h2>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#History">1History</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Types">2Types</a>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Rooted_tree">2.1Rooted tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Unrooted_tree">2.2Unrooted tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Bifurcating_tree">2.3Bifurcating tree</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Special_tree_types">2.4Special tree types</a></li>
</ul>
</li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Construction">3Construction</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Limitations">4Limitations</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#See_also">5See also</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#References">6References</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Further_reading">7Further reading</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#External_links">8External links</a>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Images">8.1Images</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#General">8.2General</a></li>
</ul>
</li>
</ul>
<h2>History[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=1" title="Edit section: History">edit</a>]</h2>
<p>The idea of a "<a href="https://en.wikipedia.org/wiki/Tree_of_life_(science)" title="Tree of life (science)">tree of life</a>" arose from ancient notions of a ladder-like progression from lower into higher forms of <a href="https://en.wikipedia.org/wiki/Life" title="Life">life</a> (such as in the <a href="https://en.wikipedia.org/wiki/Great_Chain_of_Being" title="Great Chain of Being">Great Chain of Being</a>). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book <em>Elementary Geology</em>, by Edward Hitchcock (first edition: 1840).</p>
<p><a href="https://en.wikipedia.org/wiki/Charles_Darwin" title="Charles Darwin">Charles Darwin</a> (1859) also produced one of the first illustrations and crucially popularized the notion of an <a href="https://en.wikipedia.org/wiki/Natural_selection" title="Natural selection">evolutionary "tree"</a>in his seminal book <em><a href="https://en.wikipedia.org/wiki/The_Origin_of_Species" title="The Origin of Species">The Origin of Species</a></em>. Over a century later, <a href="https://en.wikipedia.org/wiki/Evolutionary_biology" title="Evolutionary biology">evolutionary biologists</a> still use <a href="https://en.wikipedia.org/wiki/Tree_structure" title="Tree structure">tree diagrams</a> to depict <a href="https://en.wikipedia.org/wiki/Evolution" title="Evolution">evolution</a> because such diagrams effectively convey the concept that <a href="https://en.wikipedia.org/wiki/Speciation" title="Speciation">speciation</a> occurs through the <a href="https://en.wikipedia.org/wiki/Adaptation" title="Adaptation">adaptive</a> and semi<a href="https://en.wikipedia.org/wiki/Random" title="Random">random</a>splitting of lineages. Over time, species classification has become less static and more dynamic.</p>
<p>The term <em>phylogenetic</em>, or <em>phylogeny</em>, derives from the two <a href="https://en.wikipedia.org/wiki/Ancient_greek" title="Ancient greek">ancient greek</a> words <a href="https://en.wiktionary.org/wiki/%CF%86%E1%BF%A6%CE%BB%CE%BF%CE%BD#Ancient_Greek" title="wikt:φῦλον">φῦλον</a> (<em>phûlon</em>), meaning "race, lineage", and <a href="https://en.wiktionary.org/wiki/%CE%B3%CE%AD%CE%BD%CE%B5%CF%83%CE%B9%CF%82#Ancient_Greek" title="wikt:γένεσις">γένεσις</a> (<em>génesis</em>), meaning "origin, source".<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-1">[1]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-2">[2]</a></sup></p>
<h2>Types[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=2" title="Edit section: Types">edit</a>]</h2>
<h3>Rooted tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=3" title="Edit section: Rooted tree">edit</a>]</h3>
<p>A rooted phylogenetic tree (see two graphics at top) is a <a href="https://en.wikipedia.org/wiki/Directed_graph" title="Directed graph">directed</a> <a href="https://en.wikipedia.org/wiki/Tree_(data_structure)" title="Tree (data structure)">tree</a> with a unique node — the root — corresponding to the (usually <a href="https://en.wikipedia.org/wiki/Imputation_(statistics)" title="Imputation (statistics)">imputed</a>) most recent common ancestor of all the entities at the <a href="https://en.wikipedia.org/wiki/Leaf_node" title="Leaf node">leaves</a> 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 <a href="https://en.wikipedia.org/wiki/Node_(computer_science)#Nodes_and_trees" title="Node (computer science)">degree</a> 2 while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges).</p>
<p>The most common method for rooting trees is the use of an uncontroversial <a href="https://en.wikipedia.org/wiki/Outgroup_(cladistics)" title="Outgroup (cladistics)">outgroup</a>—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.</p>
<h3>Unrooted tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=4" title="Edit section: Unrooted tree">edit</a>]</h3>
<p><a href="https://en.wikipedia.org/wiki/File:MyosinUnrootedTree.jpg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/MyosinUnrootedTree.jpg/340px-MyosinUnrootedTree.jpg" style="height:240px; width:340px" /></a></p>
<p>An unrooted phylogenetic tree for <a href="https://en.wikipedia.org/wiki/Myosin" title="Myosin">myosin</a>, a <a href="https://en.wikipedia.org/wiki/Gene_family" title="Gene family">superfamily</a> of <a href="https://en.wikipedia.org/wiki/Protein" title="Protein">proteins</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Hodge_2000-3">[3]</a></sup></p>
<p>Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-4">[4]</a></sup> Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the <a href="https://en.wikipedia.org/wiki/Molecular_clock" title="Molecular clock">molecular clock</a> <a href="https://en.wikipedia.org/wiki/Hypothesis" title="Hypothesis">hypothesis</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Maher_2002-5">[5]</a></sup></p>
<h3>Bifurcating tree[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=5" title="Edit section: Bifurcating tree">edit</a>]</h3>
<p>Both rooted and unrooted phylogenetic trees can be either <a href="https://en.wikipedia.org/wiki/Bifurcation_theory" title="Bifurcation theory">bifurcating</a> or multifurcating, and either labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each <a href="https://en.wikipedia.org/wiki/Interior_node" title="Interior node">interior node</a> (that is, it forms a <a href="https://en.wikipedia.org/wiki/Binary_tree" title="Binary tree">binary tree</a>), and an unrooted bifurcating tree takes the form of an <a href="https://en.wikipedia.org/wiki/Unrooted_binary_tree" title="Unrooted binary tree">unrooted binary tree</a>, a <a href="https://en.wikipedia.org/wiki/Free_tree" title="Free tree">free tree</a> with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For labeled bifurcating trees, there are:</p>
<p>{\displaystyle (2n-3)!!={\frac {(2n-3)!}{2^{n-2}(n-2)!}}\,\,{\text{for}}\,n\geq 2}<img alt="{\displaystyle (2n-3)!!={\frac {(2n-3)!}{2^{n-2}(n-2)!}}\,\,{\text{for}}\,n\geq 2}" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/cc3ce2c88666896f262dde1714ecdf2fbf160d47" /></p>
<p>total rooted trees and</p>
<p>{\displaystyle (2n-5)!!={\frac {(2n-5)!}{2^{n-3}(n-3)!}}\,\,{\text{for}}\,n\geq 3}<img alt="{\displaystyle (2n-5)!!={\frac {(2n-5)!}{2^{n-3}(n-3)!}}\,\,{\text{for}}\,n\geq 3}" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/2d595b11feed87c05ed569f80a141e712d1105c7" /></p>
<p>total unrooted trees, where {\displaystyle n}<img alt="n" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/a601995d55609f2d9f5e233e36fbe9ea26011b3b" /> represents the number of leaf nodes. Among labeled bifurcating trees, the number of unrooted trees with {\displaystyle n}<img alt="n" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/a601995d55609f2d9f5e233e36fbe9ea26011b3b" /> leaves is equal to the number of rooted trees with {\displaystyle n-1}<img alt="n-1" src="https://wikimedia.org/api/rest_v1/media/math/render/svg/fbd0b0f32b28f51962943ee9ede4fb34198a2521" />leaves.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup></p>
<h3>Special tree types[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=6" title="Edit section: Special tree types">edit</a>]</h3>
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<p><a href="https://en.wikipedia.org/wiki/File:Question_book-new.svg"><img alt="" src="https://upload.wikimedia.org/wikipedia/en/thumb/9/99/Question_book-new.svg/50px-Question_book-new.svg.png" style="height:39px; width:50px" /></a></p>
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<p>This section <strong>does not <a href="https://en.wikipedia.org/wiki/Wikipedia:Citing_sources" title="Wikipedia:Citing sources">cite</a> any <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability">sources</a></strong>. Please help <a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit">improve this section</a> by <a href="https://en.wikipedia.org/wiki/Help:Introduction_to_referencing_with_Wiki_Markup/1" title="Help:Introduction to referencing with Wiki Markup/1">adding citations to reliable sources</a>. Unsourced material may be challenged and <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability#Burden_of_evidence" title="Wikipedia:Verifiability">removed</a>. <small><em>(October 2012)</em></small><small><em> (<a href="https://en.wikipedia.org/wiki/Help:Maintenance_template_removal" title="Help:Maintenance template removal">Learn how and when to remove this template message</a>)</em></small></p>
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<p><a href="https://en.wikipedia.org/wiki/File:Spindle_diagram.jpg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/7/76/Spindle_diagram.jpg/220px-Spindle_diagram.jpg" style="height:153px; width:220px" /></a></p>
<p>A spindle diagram, showing the evolution of the <a href="https://en.wikipedia.org/wiki/Vertebrate" title="Vertebrate">vertebrates</a> at class level, width of spindles indicating number of families. Spindle diagrams are often used in <a href="https://en.wikipedia.org/wiki/Evolutionary_taxonomy" title="Evolutionary taxonomy">evolutionary taxonomy</a>.</p>
<p><a href="https://en.wikipedia.org/wiki/File:Tree_of_life_SVG.svg"><img alt="" src="https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Tree_of_life_SVG.svg/340px-Tree_of_life_SVG.svg.png" style="height:340px; width:340px" /></a></p>
<p>A highly resolved, automatically generated <a href="https://en.wikipedia.org/wiki/Tree_of_life_(biology)" title="Tree of life (biology)">tree of life</a>, based on completely sequenced genomes.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-7">[7]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-8">[8]</a></sup></p>
<ul>
<li>A <a href="https://en.wikipedia.org/wiki/Dendrogram" title="Dendrogram">dendrogram</a> is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-9">[9]</a></sup></li>
<li>A <a href="https://en.wikipedia.org/wiki/Cladogram" title="Cladogram">cladogram</a> is a phylogenetic tree formed using <a href="https://en.wikipedia.org/wiki/Cladistics" title="Cladistics">cladistic</a> methods. This type of tree only represents a branching pattern; i.e., its branch spans do not represent time or relative amount of character change.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-10">[10]</a></sup></li>
<li>A phylogram is a phylogenetic tree that has branch spans proportional to the amount of character change.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-11">[11]</a></sup></li>
<li>A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch spans.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Santamaria2009-12">[12]</a></sup></li>
<li>A spindle diagram (often called a Romerogram after the American palaeontologist <a href="https://en.wikipedia.org/wiki/Alfred_Romer" title="Alfred Romer">Alfred Romer</a>) is the representation of the evolution and abundance of the various taxa through time.</li>
<li>A <a href="https://en.wikipedia.org/wiki/Rolf_Dahlgren" title="Rolf Dahlgren">Dahlgrenogram</a> is a diagram representing a cross section of a phylogenetic tree</li>
<li>A <a href="https://en.wikipedia.org/wiki/Phylogenetic_network" title="Phylogenetic network">phylogenetic network</a> is not strictly speaking a tree, but rather a more general <a href="https://en.wikipedia.org/wiki/Graph_(discrete_mathematics)" title="Graph (discrete mathematics)">graph</a>, or a <a href="https://en.wikipedia.org/wiki/Directed_acyclic_graph" title="Directed acyclic graph">directed acyclic graph</a> in the case of rooted networks. They are used to overcome some of the <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Limitations" title="Phylogenetic tree">limitations</a> inherent to trees.</li>
</ul>
<h2>Construction[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=7" title="Edit section: Construction">edit</a>]</h2>
<p>Main article: <a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">Computational phylogenetics</a></p>
<p>Phylogenetic trees composed with a nontrivial number of input sequences are constructed using <a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">computational phylogenetics</a> methods. Distance-matrix methods such as <a href="https://en.wikipedia.org/wiki/Neighbor-joining" title="Neighbor-joining">neighbor-joining</a> or <a href="https://en.wikipedia.org/wiki/UPGMA" title="UPGMA">UPGMA</a>, which calculate <a href="https://en.wikipedia.org/wiki/Genetic_distance" title="Genetic distance">genetic distance</a> from <a href="https://en.wikipedia.org/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">multiple sequence alignments</a>, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as <a href="https://en.wikipedia.org/wiki/ClustalW" title="ClustalW">ClustalW</a> also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. <a href="https://en.wikipedia.org/wiki/Maximum_parsimony" title="Maximum parsimony">Maximum parsimony</a> is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the <a href="https://en.wikipedia.org/wiki/Optimality_criterion" title="Optimality criterion">optimality criterion</a> of <a href="https://en.wikipedia.org/wiki/Maximum_likelihood" title="Maximum likelihood">maximum likelihood</a>, often within a <a href="https://en.wikipedia.org/wiki/Bayesian_inference" title="Bayesian inference">Bayesian Framework</a>, and apply an explicit model of evolution to phylogenetic tree estimation.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup> Identifying the optimal tree using many of these techniques is <a href="https://en.wikipedia.org/wiki/NP-hard" title="NP-hard">NP-hard</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Felsenstein-6">[6]</a></sup> so <a href="https://en.wikipedia.org/wiki/Heuristic" title="Heuristic">heuristic</a> search and <a href="https://en.wikipedia.org/wiki/Optimization_(mathematics)" title="Optimization (mathematics)">optimization</a> methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data.</p>
<p>Tree-building methods can be assessed on the basis of several criteria:<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-13">[13]</a></sup></p>
<ul>
<li>efficiency (how long does it take to compute the answer, how much memory does it need?)</li>
<li>power (does it make good use of the data, or is information being wasted?)</li>
<li>consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)</li>
<li>robustness (does it cope well with violations of the assumptions of the underlying model?)</li>
<li>falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)</li>
</ul>
<p>Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using <a href="https://en.wikipedia.org/wiki/T-theory" title="T-theory">T-theory</a>.<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-14">[14]</a></sup></p>
<h2>Limitations[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=8" title="Edit section: Limitations">edit</a>]</h2>
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<p>This section <strong>needs additional citations for <a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability">verification</a></strong>. Please help <a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit">improve this article</a> by <a href="https://en.wikipedia.org/wiki/Help:Introduction_to_referencing_with_Wiki_Markup/1" title="Help:Introduction to referencing with Wiki Markup/1">adding citations to reliable sources</a>. Unsourced material may be challenged and removed. <small><em>(October 2012)</em></small><small><em> (<a href="https://en.wikipedia.org/wiki/Help:Maintenance_template_removal" title="Help:Maintenance template removal">Learn how and when to remove this template message</a>)</em></small></p>
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<p>Although phylogenetic trees produced on the basis of sequenced <a href="https://en.wikipedia.org/wiki/Gene" title="Gene">genes</a> or <a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genomic</a> data in different species can provide evolutionary insight, they have important limitations. Most importantly, they do not necessarily accurately represent the evolutionary history of the included taxa. In fact, they are literally scientific <a href="https://en.wikipedia.org/wiki/Hypotheses" title="Hypotheses">hypotheses</a>, subject to <a href="https://en.wikipedia.org/wiki/Falsifiability" title="Falsifiability">falsification</a> by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based is <a href="https://en.wikipedia.org/wiki/Signal_noise" title="Signal noise">noisy</a>;<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Townsend_2012-15">[15]</a></sup> the analysis can be confounded by <a href="https://en.wikipedia.org/wiki/Genetic_recombination" title="Genetic recombination">genetic recombination</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Arenas_2010-16">[16]</a></sup> <a href="https://en.wikipedia.org/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">horizontal gene transfer</a>,<sup><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_note-Woese_2002-17">[17]</a></sup><a href="https://en.wikipedia.org/wiki/Hybrid_(biology)" title="Hybrid (biology)">hybridisation</a> between species that were not nearest neighbors on the tree before hybridisation takes place, <a href="https://en.wikipedia.org/wiki/Convergent_evolution" title="Convergent evolution">convergent evolution</a>, and <a href="https://en.wikipedia.org/wiki/Conserved_sequence" title="Conserved sequence">conserved sequences</a>.</p>
<p>Also, there are problems in basing the analysis on a single type of character, such as a single <a href="https://en.wikipedia.org/wiki/Gene" title="Gene">gene</a> or <a href="https://en.wikipedia.org/wiki/Protein" title="Protein">protein</a> or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This is most true of genetic material that is subject to lateral gene transfer and <a href="https://en.wikipedia.org/wiki/Genetic_recombination" title="Genetic recombination">recombination</a>, where different <a href="https://en.wikipedia.org/wiki/Haplotype" title="Haplotype">haplotype</a> blocks can have different histories. In general, the output tree of a phylogenetic analysis is an estimate of the <em>character'</em>s phylogeny (i.e. a gene tree) and not the phylogeny of the <a href="https://en.wikipedia.org/wiki/Taxa" title="Taxa">taxa</a> (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use a combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be expected to evolve under different selective regimes, so that <a href="https://en.wikipedia.org/wiki/Homoplasy" title="Homoplasy">homoplasy</a> (false <a href="https://en.wikipedia.org/wiki/Homology_(biology)" title="Homology (biology)">homology</a>) would be unlikely to result from natural selection.</p>
<p>When extinct species are included in a tree, they are <a href="https://en.wikipedia.org/wiki/Leaf_node" title="Leaf node">terminal nodes</a>, as it is unlikely that they are direct ancestors of any extant species. Skepticism might be applied when extinct species are included in trees that are wholly or partly based on DNA sequence data, because little useful "<a href="https://en.wikipedia.org/wiki/Ancient_DNA" title="Ancient DNA">ancient DNA</a>" is preserved for longer than 100,000 years, and except in the most unusual circumstances no DNA sequences long enough for use in phylogenetic analyses have yet been recovered from material over 1 million years old.<sup>[<em><a href="https://en.wikipedia.org/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed">citation needed</a></em>]</sup></p>
<p>The range of useful DNA materials has expanded with advances in extraction and sequencing technologies. Development of technologies able to infer sequences from smaller fragments, or from spatial patterns of DNA degradation products, would further expand the range of DNA considered useful.</p>
<p>In some organisms, <a href="https://en.wikipedia.org/wiki/Endosymbiont" title="Endosymbiont">endosymbionts</a> have an independent genetic history from the host.</p>
<p><a href="https://en.wikipedia.org/wiki/Phylogenetic_network" title="Phylogenetic network">Phylogenetic networks</a> are used when bifurcating trees are not suitable, due to these complications which suggest a more <a href="https://en.wikipedia.org/wiki/Reticulate" title="Reticulate">reticulate</a> evolutionary history of the organisms sampled.</p>
<h2>See also[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=9" title="Edit section: See also">edit</a>]</h2>
<ul>
<li><a href="https://en.wikipedia.org/wiki/File:Tree_of_life.svg"><img alt="icon" src="https://upload.wikimedia.org/wikipedia/commons/thumb/0/09/Tree_of_life.svg/32px-Tree_of_life.svg.png" style="height:27px; width:32px" /></a><a href="https://en.wikipedia.org/wiki/Portal:Evolutionary_biology" title="Portal:Evolutionary biology">Evolutionary biology portal</a></li>
</ul>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Cladistics" title="Cladistics">Cladistics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Comparative_phylogenetics" title="Comparative phylogenetics">Comparative phylogenetics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Computational_phylogenetics" title="Computational phylogenetics">Computational phylogenetics</a></li>
<li><a href="https://en.wikipedia.org/wiki/Evolutionary_taxonomy" title="Evolutionary taxonomy">Evolutionary taxonomy</a></li>
<li><a href="https://en.wikipedia.org/wiki/Evolutionary_biology" title="Evolutionary biology">Evolutionary biology</a></li>
<li><a href="https://en.wikipedia.org/wiki/Generalized_tree_alignment" title="Generalized tree alignment">Generalized tree alignment</a></li>
<li><a href="https://en.wikipedia.org/wiki/List_of_phylogenetics_software" title="List of phylogenetics software">List of phylogenetics software</a></li>
<li><a href="https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software" title="List of phylogenetic tree visualization software">List of phylogenetic tree visualization software</a></li>
<li><a href="https://en.wikipedia.org/wiki/Phylogenetic_comparative_methods" title="Phylogenetic comparative methods">Phylogenetic comparative methods</a></li>
</ul>
<h2>References[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=10" title="Edit section: References">edit</a>]</h2>
<ol>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-1" title="Jump up">^</a></strong> <cite>Bailly, Anatole (1981-01-01). <a href="https://www.worldcat.org/oclc/461974285" rel="nofollow"><em>Abrégé du dictionnaire grec français</em></a>. Paris: Hachette. <a href="https://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number">ISBN</a> <a href="https://en.wikipedia.org/wiki/Special:BookSources/978-2010035289" title="Special:BookSources/978-2010035289">978-2010035289</a>. <a href="https://en.wikipedia.org/wiki/OCLC" title="OCLC">OCLC</a> <a href="https://www.worldcat.org/oclc/461974285" rel="nofollow">461974285</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-2" title="Jump up">^</a></strong> <cite>Bailly, Anatole. <a href="http://www.tabularium.be/bailly/" rel="nofollow">"Greek-french dictionary online"</a>. <em>www.tabularium.be</em>. <a href="https://web.archive.org/web/20140421003247/http://www.tabularium.be/bailly/" rel="nofollow">Archived</a> from the original on April 21, 2014. Retrieved March 2, 2018.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Hodge_2000_3-0" title="Jump up">^</a></strong> <cite>Hodge T, Cope M (1 October 2000). <a href="http://jcs.biologists.org/cgi/content/full/113/19/3353" rel="nofollow">"A myosin family tree"</a>. <em>J Cell Sci</em>. <strong>113</strong> (19): 3353–4. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/10984423" rel="nofollow">10984423</a>. <a href="https://web.archive.org/web/20070930043742/http://jcs.biologists.org/cgi/content/full/113/19/3353" rel="nofollow">Archived</a> from the original on 30 September 2007.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-4" title="Jump up">^</a></strong> <cite><a href="https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html" rel="nofollow">"Archived copy"</a>. <a href="https://web.archive.org/web/20140414030413/http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html" rel="nofollow">Archived</a> from the original on 2014-04-14. Retrieved 2014-05-26.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Maher_2002_5-0" title="Jump up">^</a></strong> <cite>Maher BA (2002). <a href="http://www.the-scientist.com/yr2002/sep/research1_020916.html" rel="nofollow">"Uprooting the Tree of Life"</a>. <em>The Scientist</em>. <strong>16</strong>: 18. <a href="https://web.archive.org/web/20031002231607/http://www.the-scientist.com/yr2002/sep/research1_020916.html" rel="nofollow">Archived</a> from the original on 2003-10-02.</cite></li>
<li>^ <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-0">Jump up to:<sup><em><strong>a</strong></em></sup></a> <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-1"><sup><em><strong>b</strong></em></sup></a> <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Felsenstein_6-2"><sup><em><strong>c</strong></em></sup></a> Felsenstein J. (2004). <em>Inferring Phylogenies</em> Sinauer Associates: Sunderland, MA.</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-7" title="Jump up">^</a></strong> <cite>Letunic, Ivica; <a href="https://en.wikipedia.org/wiki/Peer_Bork" title="Peer Bork">Bork, Peer</a> (1 January 2007). <a href="http://itol.embl.de/help/17050570.pdf" rel="nofollow">"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation"</a> (PDF). <em><a href="https://en.wikipedia.org/wiki/Bioinformatics_(journal)" title="Bioinformatics (journal)">Bioinformatics</a></em>. Cambridge. <strong>23</strong> (1): 127–128. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtl529" rel="nofollow">10.1093/bioinformatics/btl529</a>. <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number" title="International Standard Serial Number">ISSN</a> <a href="https://www.worldcat.org/issn/1367-4803" rel="nofollow">1367-4803</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/17050570" rel="nofollow">17050570</a>. <a href="https://web.archive.org/web/20151129010406/http://itol.embl.de/help/17050570.pdf" rel="nofollow">Archived</a> (PDF) from the original on November 29, 2015. Retrieved 2015-07-21.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-8" title="Jump up">^</a></strong> <cite>Ciccarelli, FD; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006). <a href="http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf" rel="nofollow">"Toward automatic reconstruction of a highly resolved tree of life"</a> (Submitted manuscript). <em>Science</em>. <strong>311</strong>(5765): 1283–7. <a href="https://en.wikipedia.org/wiki/Bibcode" title="Bibcode">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2006Sci...311.1283C" rel="nofollow">2006Sci...311.1283C</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1126%2Fscience.1123061" rel="nofollow">10.1126/science.1123061</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/16513982" rel="nofollow">16513982</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-9" title="Jump up">^</a></strong> <cite>Fox, Emily. <a href="https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram" rel="nofollow">"The dendrogram"</a>. <em>coursea</em>. coursea. <a href="https://web.archive.org/web/20170928060157/https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram" rel="nofollow">Archived</a>from the original on 28 September 2017. Retrieved 28 September2017.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-10" title="Jump up">^</a></strong> Mayr, Ernst (2009)"Cladistic analysis or cladistic classification?". Journal of Zoological Systematics and Evolutionary Research. 12: 94–128. doi:10.1111/j.1439-0469.1974.tb00160.x..</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-11" title="Jump up">^</a></strong> Antonio Soares, Ricardo Râbelo, Alexandre Delbem, Optimization based on phylogram analysis, In Expert Systems with Applications, Volume 78, 2017, Pages 32-50, ISSN 0957-4174, <a href="https://doi.org/10.1016/j.eswa.2017.02.012" rel="nofollow">https://doi.org/10.1016/j.eswa.2017.02.012</a>.</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Santamaria2009_12-0" title="Jump up">^</a></strong> <cite>Santamaria, R.; Theron, R. (2009-05-26). <a href="https://academic.oup.com/bioinformatics/article/25/15/1970/212219" rel="nofollow">"Treevolution: visual analysis of phylogenetic trees"</a>. <em>Bioinformatics</em>. <strong>25</strong> (15): 1970–1971. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtp333" rel="nofollow">10.1093/bioinformatics/btp333</a>. <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number" title="International Standard Serial Number">ISSN</a> <a href="https://www.worldcat.org/issn/1367-4803" rel="nofollow">1367-4803</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-13" title="Jump up">^</a></strong> <cite>Penny, D.; Hendy, M. D.; <a href="https://en.wikipedia.org/wiki/Mike_Steel_(mathematician)" title="Mike Steel (mathematician)">Steel, M. A.</a> (1992). "Progress with methods for constructing evolutionary trees". <em>Trends in Ecology and Evolution</em>. <strong>7</strong> (3): 73–79. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1016%2F0169-5347%2892%2990244-6" rel="nofollow">10.1016/0169-5347(92)90244-6</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/21235960" rel="nofollow">21235960</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-14" title="Jump up">^</a></strong> A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. <em>Documenta Mathematica</em> <em>LSU 2001</em>: 121-139</li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Townsend_2012_15-0" title="Jump up">^</a></strong> <cite>Townsend JP, Su Z, Tekle Y (2012). "Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny". <em>Genetics</em>. <strong>61</strong> (5): 835–849. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1093%2Fsysbio%2Fsys036" rel="nofollow">10.1093/sysbio/sys036</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/22389443" rel="nofollow">22389443</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Arenas_2010_16-0" title="Jump up">^</a></strong> <cite>Arenas M, Posada D (2010). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865913" rel="nofollow">"The effect of recombination on the reconstruction of ancestral sequences"</a>. <em>Genetics</em>. <strong>184</strong> (4): 1133–1139. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1534%2Fgenetics.109.113423" rel="nofollow">10.1534/genetics.109.113423</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865913" rel="nofollow">2865913</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/20124027" rel="nofollow">20124027</a>.</cite></li>
<li><strong><a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#cite_ref-Woese_2002_17-0" title="Jump up">^</a></strong> <cite>Woese C (2002). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369" rel="nofollow">"On the evolution of cells"</a>. <em>Proc Natl Acad Sci USA</em>. <strong>99</strong> (13): 8742–7. <a href="https://en.wikipedia.org/wiki/Bibcode" title="Bibcode">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2002PNAS...99.8742W" rel="nofollow">2002PNAS...99.8742W</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1073%2Fpnas.132266999" rel="nofollow">10.1073/pnas.132266999</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124369" rel="nofollow">124369</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/12077305" rel="nofollow">12077305</a>.</cite></li>
</ol>
<h2>Further reading[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=11" title="Edit section: Further reading">edit</a>]</h2>
<ul>
<li>Schuh, R. T. and A. V. Z. Brower. 2009. <em>Biological Systematics: principles and applications (2nd edn.)</em> <a href="https://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number">ISBN</a> <a href="https://en.wikipedia.org/wiki/Special:BookSources/978-0-8014-4799-0" title="Special:BookSources/978-0-8014-4799-0">978-0-8014-4799-0</a></li>
<li><a href="https://en.wikipedia.org/wiki/Manuel_Lima" title="Manuel Lima">Manuel Lima</a>, <em>The Book of Trees: Visualizing Branches of Knowledge</em>, 2014, Princeton Architectural Press, New York.</li>
<li><a href="https://en.wikipedia.org/wiki/MEGA,_Molecular_Evolutionary_Genetics_Analysis" title="MEGA, Molecular Evolutionary Genetics Analysis">MEGA</a>, a free software to draw phylogenetic trees.</li>
</ul>
<h2>External links[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=12" title="Edit section: External links">edit</a>]</h2>
<table>
<tbody>
<tr>
<td><img alt="" src="https://upload.wikimedia.org/wikipedia/en/thumb/4/4a/Commons-logo.svg/30px-Commons-logo.svg.png" style="height:40px; width:30px" /></td>
<td>Wikimedia Commons has media related to <em><strong><a href="https://commons.wikimedia.org/wiki/Category:Phylogenetic_tree_of_life" title="commons:Category:Phylogenetic tree of life">Phylogenetic tree</a></strong></em>.</td>
</tr>
</tbody>
</table>
<h3>Images[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=13" title="Edit section: Images">edit</a>]</h3>
<ul>
<li><a href="https://www.webcitation.org/66QTvQVdZ?url=http://ycc.biosci.arizona.edu/nomenclature_system/fig1.html" rel="nofollow">Human Y-Chromosome 2002 Phylogenetic Tree</a></li>
<li><a href="http://itol.embl.de/" rel="nofollow">iTOL: Interactive Tree Of Life</a></li>
<li><a href="http://picbreeder.com/tol.php" rel="nofollow">Phylogenetic Tree of Artificial Organisms Evolved on Computers</a></li>
<li><a href="https://web.archive.org/web/20110210200039/http://phylogram.org/" rel="nofollow">Miyamoto and Goodman's Phylogram of Eutherian Mammals</a></li>
</ul>
<h3>General[<a href="https://en.wikipedia.org/w/index.php?title=Phylogenetic_tree&action=edit&section=14" title="Edit section: General">edit</a>]</h3>
<ul>
<li>An overview of different methods of tree visualization is available at <cite>Page, R. D. M. (2011). "Space, time, form: Viewing the Tree of Life". <em>Trends in Ecology & Evolution</em>. <strong>27</strong> (2): 113–120. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1016%2Fj.tree.2011.12.002" rel="nofollow">10.1016/j.tree.2011.12.002</a>.</cite></li>
<li><a href="http://www.discoverlife.org/tree" rel="nofollow">Discover Life</a> An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project</li>
<li><a href="https://web.archive.org/web/20071114093618/http://www.ohiou.edu/phylocode/index.html" rel="nofollow">PhyloCode</a></li>
<li><a href="http://webarchive.loc.gov/all/20011109204837/http://www.mrc-lmb.cam.ac.uk/myosin/trees/trees.html" rel="nofollow">A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree</a></li>
<li><a href="http://tolweb.org/tree" rel="nofollow">Tree of Life Web Project</a></li>
<li><a href="http://www.trex.uqam.ca/" rel="nofollow">Phylogenetic inferring on the T-REX server</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/" rel="nofollow">NCBI's Taxonomy Database</a><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/" rel="nofollow">[1]</a></li>
<li><a href="https://web.archive.org/web/20140525220921/http://ete.cgenomics.org/" rel="nofollow">ETE: A Python Environment for Tree Exploration</a> This is a programming library to analyze, manipulate and visualize phylogenetic trees. <a href="http://www.biomedcentral.com/1471-2105/11/24" rel="nofollow">Ref.</a></li>
<li><a href="http://supfam.org/SUPERFAMILY/sTOL" rel="nofollow">A daily-updated tree of (sequenced) life</a> <cite>Fang, H.; Oates, M. E.; Pethica, R. B.; Greenwood, J. M.; Sardar, A. J.; Rackham, O. J. L.; Donoghue, P. C. J.; Stamatakis, A.; De Lima Morais, D. A.; Gough, J. (2013). "A daily-updated tree of (sequenced) life as a reference for genome research". <em>Scientific Reports</em>. <strong>3</strong>: 2015. <a href="https://en.wikipedia.org/wiki/Bibcode" title="">Bibcode</a>:<a href="http://adsabs.harvard.edu/abs/2013NatSR...3E2015F" rel="nofollow">2013NatSR...3E2015F</a>. <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a>:<a href="https://doi.org/10.1038%2Fsrep02015" rel="nofollow">10.1038/srep02015</a>. <a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a> <a href="https://www.ncbi.nlm.nih.gov/pubmed/23778980" rel="nofollow">23778980</a>.</cite></li>
</ul>