TheInfoList

A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching
diagram A diagram is a symbolic representation Representation may refer to: Law and politics *Representation (politics) Political representation is the activity of making citizens "present" in public policy making processes when political actors act in ...

or a
tree In botany, a tree is a perennial plant with an elongated Plant stem, stem, or trunk (botany), trunk, supporting branches and leaves in most species. In some usages, the definition of a tree may be narrower, including only wood plants with se ...
showing the
evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

ary relationships among various biological
species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individu ...

or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating
common ancestry Common descent is a concept in evolutionary biology Evolutionary biology is the subfield of biology that studies the evolution, evolutionary processes (natural selection, common descent, speciation) that produced the Biodiversity, diversity ...
. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred
most recent common ancestor In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
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
bioinformatics Bioinformatics () is an field that develops methods and s for understanding data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines , , , and to analyze and interpret ...

,
systematics Biological Biology is the natural science Natural science is a branch of science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic enterprise that Scientific method, builds and Taxonomy (general), or ...
, and
phylogenetics In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms ...

. ''Unrooted'' trees illustrate only the relatedness of the
leaf nodes In computer science Computer science deals with the theoretical foundations of information, algorithms and the architectures of its computation as well as practical techniques for their application. Computer science is the study of Algo ...
and do not require the ancestral root to be known or inferred.

# History

The idea of a "
tree of life#REDIRECT Tree of life The tree of life is a fundamental widespread mytheme or archetype in many of the world's mythology, mythologies, religion, religious and philosophy, philosophical traditions. It is closely related to the concept of the s ...
" arose from ancient notions of a ladder-like progression from lower into higher forms of
life Life is a characteristic that distinguishes physical entities A bubble of exhaled gas in water In common usage and classical mechanics, a physical object or physical body (or simply an object or body) is a collection of matter within a ...

(such as in the
Great Chain of Being The Great Chain of Being is a hierarchical structure of all matter and life, thought by medieval Christianity Christianity is an Abrahamic religions, Abrahamic Monotheism, monotheistic religion based on the Life of Jesus in the New Testament, ...
). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book ''Elementary Geology'', by
Edward Hitchcock Edward Hitchcock (May 24, 1793 – February 27, 1864) was an American geologist and the third President of Amherst College (1845–1854). Life Born to poor parents, he attended newly founded Deerfield Academy, where he was later principal, fr ...

(first edition: 1840).
Charles Darwin Charles Robert Darwin (; ; 12 February 1809 – 19 April 1882) was an English natural history#Before 1900, naturalist, geologist and biologist, best known for his contributions to the science of evolution. His proposition that all sp ...

(1859) also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book ''
The Origin of Species ''On the Origin of Species'' (or, more completely, ''On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life''),The book's full original title was ''On the Origin of Species by Mea ...
''. Over a century later,
evolutionary biologist Evolutionary biology is the subfield of biology that studies the evolutionary processes ( natural selection, common descent, speciation) that produced the Biodiversity, diversity of life on Earth. In the 1930s, the discipline of evolutionary b ...
s still use s to depict
evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

because such diagrams effectively convey the concept that
speciation Speciation is the evolution Evolution is change in the Heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes that are ...

occurs through the and semi
random In common parlance, randomness is the apparent or actual lack of pattern or predictability in events. A random sequence of events, symbols or steps often has no :wikt:order, order and does not follow an intelligible pattern or combination. I ...

splitting of lineages. Over time, species classification has become less static and more dynamic. The term ''phylogenetic'', or ''phylogeny'', derives from the two
ancient greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ), refers collectively to the diale ...
words (), meaning "race, lineage", and (), meaning "origin, source".

# Properties

## Rooted tree

A rooted phylogenetic tree (see two graphics at top) is a
directed Director may refer to: Literature * Director (magazine), ''Director'' (magazine), a British magazine * The Director (novel), ''The Director'' (novel), a 1971 novel by Henry Denker * The Director (play), ''The Director'' (play), a 2000 play by Nanc ...

tree In botany, a tree is a perennial plant with an elongated Plant stem, stem, or trunk (botany), trunk, supporting branches and leaves in most species. In some usages, the definition of a tree may be narrower, including only wood plants with se ...
with a unique node — the root — corresponding to the (usually imputed) most recent common ancestor of all the entities at the
leaves A leaf (plural leaves) is the principal lateral appendage of the vascular plant plant stem, stem, usually borne above ground and specialized for photosynthesis. The leaves, stem, flower and fruit together form the shoot system. Leaves are ...
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
degree Degree may refer to: As a unit of measurement * Degree symbol (°), a notation used in science, engineering, and mathematics * Degree (angle), a unit of angle measurement * Degree (temperature), any of various units of temperature measurement ...
2, while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges). The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.

## Unrooted tree

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. 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
molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Thou ...
hypothesis A hypothesis (plural hypotheses) is a proposed explanation An explanation is a set of statements usually constructed to describe a set of facts which clarifies the causes, context Context may refer to: * Context (language use), the rel ...
.

## Bifurcating versus multifurcating

Both rooted and unrooted trees can be either bifurcating or multifurcating. A rooted bifurcating tree has exactly two descendants arising from each
interior node In computer science, a tree is a widely used abstract data type that simulates a hierarchical tree structure, with a root value and subtrees of children with a #Terminology, parent node, represented as a set of linked Node (computer science), nod ...
(that is, it forms a
binary tree In computer science Computer science deals with the theoretical foundations of information, algorithms and the architectures of its computation as well as practical techniques for their application. Computer science is the study of , ...

), and an unrooted bifurcating tree takes the form of an
unrooted binary tree In mathematics and computer science, an unrooted binary tree is an free tree, unrooted tree in which each vertex (graph theory), vertex has either one or three neighbors. Definitions A free tree or unrooted tree is a connected graph, connected und ...
, a free tree 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.

## Labeled versus unlabeled

Both rooted and unrooted trees can be either labeled or unlabeled. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. Some sequence-based trees built from a small genomic locus, such as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes.

## Enumerating trees

The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more labeled than unlabeled trees, more multifurcating than bifurcating 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 bifurcating labeled trees, the total number of rooted trees is: :$\left(2n-3\right)!! = \frac$ for $n \ge 2$, $n$ represents the number of leaf nodes. For bifurcating labeled trees, the total number of unrooted trees is: :$\left(2n-5\right)!! = \frac$ for $n \ge 3$. Among labeled bifurcating trees, the number of unrooted trees with $n$ leaves is equal to the number of rooted trees with $n-1$ leaves.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. The number of rooted trees grows quickly as a function of the number of tips. For 10 tips, there are more than $34 \times 10^6$ possible bifurcating trees, and the number of multifurcating trees rises faster, with ca. 7 times as many of the latter as of the former. style="text-align: left; margin-left: auto; margin-right: auto; border: none;" , + Counting trees. ! Labeled
leaves !! Binary
unrooted trees !! Binary
rooted trees !! Multifurcating
rooted trees !! All possible
rooted trees , - , 1 , , 1 , , 1 , , 0 , , 1 , - , 2 , , 1 , , 1 , , 0 , , 1 , - , 3 , , 1 , , 3 , , 1 , , 4 , - , 4 , , 3 , , 15 , , 11 , , 26 , - , 5 , , 15 , , 105 , , 131 , , 236 , - , 6 , , 105 , , 945 , , 1,807 , , 2,752 , - , 7 , , 945 , , 10,395 , , 28,813 , , 39,208 , - , 8 , , 10,395 , , 135,135 , , 524,897 , , 660,032 , - , 9 , , 135,135 , , 2,027,025 , , 10,791,887 , , 12,818,912 , - , 10 , , 2,027,025 , , 34,459,425 , , 247,678,399 , , 282,137,824 , -

# Special tree types

## Dendrogram

A
dendrogram File:Phylogenetic tree.svg, A dendrogram of the Tree of Life. This phylogenetic tree is adapted from Woese et al. rRNA analysis. The vertical line at bottom represents the last universal common ancestor (LUCA). A dendrogram is a diagram repre ...
is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree.

A
cladogram A cladogram (from Greek ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics Cladistics (, from Greek language, Greek , ''kládos'', "branch") is an approach to Taxonomy (biology), biological classification in whi ...

only represents a branching pattern; i.e., its branch lengths do not represent time or relative amount of character change, and its internal nodes do not represent ancestors.

## Phylogram

A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change. A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths.

## Dahlgrenogram

A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree

## Phylogenetic network

A
phylogenetic network A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to descri ...
is not strictly speaking a tree, but rather a more general
graph Graph may refer to: Mathematics *Graph (discrete mathematics), a structure made of vertices and edges **Graph theory, the study of such graphs and their properties *Graph (topology), a topological space resembling a graph in the sense of discret ...
, or a
directed acyclic graph In mathematics Mathematics (from Greek: ) includes the study of such topics as numbers (arithmetic and number theory), formulas and related structures (algebra), shapes and spaces in which they are contained (geometry), and quantities and ...

in the case of rooted networks. They are used to overcome some of the
limitationsLimitation may refer to: *A disclaimer for research done in an experiment An experiment is a procedure carried out to support, refute, or validate a hypothesis. Experiments provide insight into Causality, cause-and-effect by demonstrating what ...
inherent to trees.

## Spindle diagram

A spindle diagram, or bubble diagram, is often called a romerogram, after its popularisation by the American palaeontologist
Alfred Romer Alfred Sherwood Romer (December 28, 1894 – November 5, 1973) was an American paleontologist Paleontology, also spelled palaeontology or palæontology (), is the scientific study of life that existed prior to, and sometimes including, the st ...
. It represents taxonomic diversity (horizontal width) against
geological time The geologic time scale (GTS) is a system of chronological datingChronological dating, or simply dating, is the process of attributing to an object or event a date in the past, allowing such object or event to be located in a previously establish ...

(vertical axis) in order to reflect the variation of abundance of various taxa through time. However, a spindle diagram is not an evolutionary tree: the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon and have the disadvantage of involving the
paraphyly In taxonomy (general), taxonomy, a group is paraphyletic if it consists of the group's most recent common ancestor, last common ancestor and all its descendants, but excluding a few—typically only one or two—Monophyly, monophyletic subgroup ...
of the parental group. This type of diagram is no longer used in the form originally proposed.

## Coral of life

Darwin also mentioned that the ''coral'' may be a more suitable metaphor than the ''tree''. Indeed, phylogenetic corals are useful for portraying past and present life, and they have some advantages over trees (anastomoses allowed, etc.).

# Construction

Phylogenetic trees composed with a nontrivial number of input sequences are constructed using
computational phylogenetics Computational phylogenetics is the application of computational algorithm In and , an algorithm () is a finite sequence of , computer-implementable instructions, typically to solve a class of problems or to perform a computation. Algorithms ...
methods. Distance-matrix methods such as
neighbor-joining In bioinformatics, neighbor joining is a bottom-up (agglomerative) Cluster analysis, clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually used for trees based on DNA or protein primary ...
or
UPGMA UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. The method is generally attributed to Robert R. Sokal, Sokal and Charles Duncan Michener, Michener. The UPGMA method is ...

, which calculate
genetic distance Genetic distance is a measure of the genetic divergence between species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is ...
from
multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment In bioinformatics Bioinformatics () is an field that develops methods and s for understanding data, in particular when the data sets are la ...
s, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as
ClustalW Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its alg ...
also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction.
Maximum parsimony In phylogenetics In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiol ...
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 In statistics, an optimality criterion provides a measure of the fit of the data to a given hypothesis, to aid in model selection. A statistical model, model is designated as the "best" of the candidate models if it gives the best value of an object ...
of
maximum likelihood In statistics, maximum likelihood estimation (MLE) is a method of estimating Estimation (or estimating) is the process of finding an estimate, or approximation An approximation is anything that is intentionally similar but not exactly equa ...
, often within a Bayesian framework, and apply an explicit model of evolution to phylogenetic tree estimation. Identifying the optimal tree using many of these techniques is
NP-hard In computational complexity theory Computational complexity theory focuses on classifying computational problem In theoretical computer science An artistic representation of a Turing machine. Turing machines are used to model general computin ...
, so
heuristic A heuristic (; ), or heuristic technique, is any approach to or that employs a practical method that is not guaranteed to be , perfect, or , but is nevertheless sufficient for reaching an immediate, short-term goal or . Where finding an optimal ...
search and
optimization File:Nelder-Mead Simionescu.gif, Nelder-Mead minimum search of Test functions for optimization, Simionescu's function. Simplex vertices are ordered by their values, with 1 having the lowest ( best) value., alt= Mathematical optimization (alter ...
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: * 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.

## 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 format * Newick format

# Limitations of phylogenetic analysis

Although phylogenetic trees produced on the basis of sequenced
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

s or
genomic Genomics is an interdisciplinary field of focusing on the structure, function, evolution, mapping, and editing of s. A genome is an organism's complete set of , including all of its genes as well as its hierarchical, three-dimensional structur ...

data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly, the trees that they generate are not necessarily correct – they do not necessarily accurately represent the evolutionary history of the included taxa. As with any scientific result, they are subject to falsification by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based may be noisy; the analysis can be confounded by
genetic recombination Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, ph ...
,
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
,
hybrid Hybrid may refer to: Economics and finance * Hybrid market, a system allowing stock trades to be completed either electronically or manually * Hybrid security, a type of economic instrument Technology Electrical power generation * Hybrid generato ...
isation between species that were not nearest neighbors on the tree before hybridisation takes place,
convergent evolution Convergent evolution is the independent evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; eithe ...
, and
conserved sequence In evolutionary biology, conserved sequences are identical or similar Sequence (biology), sequences in nucleic acids (DNA sequence, DNA and RNA) or peptide sequence, proteins across species (homology (biology)#Orthology, orthologous sequences), ...
s. Also, there are problems in basing an analysis on a single type of character, such as a single
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

or
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

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 recombination, where different
haplotype A haplotype (haploid Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called hi ...
blocks can have different histories. In these types of analysis, the output tree of a phylogenetic analysis of a single gene is an estimate of the gene's phylogeny (i.e. a gene tree) and not the phylogeny of the
taxa In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
(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
homoplasy Homoplasy, in biology and phylogenetics, is when a Phenotypic trait, trait has been gained or lost independently in separate lineages over the course of evolution. This is different from Homology (biology), homology, which is the similarity of trait ...

(false homology) would be unlikely to result from natural selection. When extinct species are included as terminal nodes in an analysis (rather than, for example, to constrain internal nodes), they are considered not to represent direct ancestors of any extant species. Extinct species do not typically contain high-quality
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

. 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. Phylogenetic trees can also be inferred from a range of other data types, including morphology, the presence or absence of particular types of genes, insertion and deletion events – and any other observation thought to contain an evolutionary signal.
Phylogenetic network A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to descri ...
s are used when bifurcating trees are not suitable, due to these complications which suggest a more reticulate evolutionary history of the organisms sampled.

*
Clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyly, monophyletic – that is, composed of a common ancestor and all its lineage (evolution), lineal descendants - on a phylogenetic tree. R ...

*
Cladistics Cladistics (; ) is an approach to biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), circumscribing) and classifying groups of biological organisms based on shared ch ...

*
Computational phylogenetics Computational phylogenetics is the application of computational algorithm In and , an algorithm () is a finite sequence of , computer-implementable instructions, typically to solve a class of problems or to perform a computation. Algorithms ...
*
Evolutionary biology Evolutionary biology is the subfield of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interacti ...
*
Evolutionary taxonomy Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), circumscribing) and classi ...
* Generalized tree alignment *
List of phylogenetics software This list of phylogenetics software is a compilation of computational phylogenetics Computational phylogenetics is the application of computational algorithm of an algorithm (Euclid's algorithm) for calculating the greatest common divisor (g.c.d ...
* List of phylogenetic tree visualization software *
PANDIT A pandit ( sa, पण्डित, paṇḍita; hi, पंडित; also spelled pundit, pronounced ; abbreviated Pt. or Pdt.) is a man with specialised knowledge or a teacher of any field of knowledge in Hinduism Hinduism () is an I ...
, a biological database covering protein domains *
Phylogenetic comparative methods Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages ( phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin C ...

# References

* Schuh, R. T. and A. V. Z. Brower. 2009. ''Biological Systematics: principles and applications (2nd edn.)'' *
Manuel Lima Manuel Lima FRSA (born May 3, 1978) is a Portuguese-American designer, author, and lecturer known for his work in information visualization and visual culture. WIRED describes Lima as “the man who turns data into art” and Forbes magazine says " ...
, ''The Book of Trees: Visualizing Branches of Knowledge'', 2014, Princeton Architectural Press, New York. *
MEGA Mega or MEGA may refer to: Science * mega-, the SI prefix for one million (106, symbol M) * Mega (number), a certain very large integer in Steinhaus–Moser notation * "mega-" a prefix meaning "large" that is List of commonly used taxonomic affi ...
, a free software to draw phylogenetic trees. * Gontier, N. 2011. "Depicting the Tree of Life: the Philosophical and Historical Roots of Evolutionary Tree Diagrams." Evolution, Education, Outreach 4: 515–538.

## Images

Human Y-Chromosome 2002 Phylogenetic TreeiTOL: Interactive Tree Of LifePhylogenetic Tree of Artificial Organisms Evolved on ComputersMiyamoto and Goodman's Phylogram of Eutherian Mammals

## General

*An overview of different methods of tree visualization is available at
OneZoom: Tree of Life – all living species as intuitive and zoomable fractal explorer (responsive design)Discover Life
An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project

* ttp://tolweb.org/tree Tree of Life Web Projectbr>Phylogenetic inferring on the T-REX serverNCBI's Taxonomy Database
https://www.ncbi.nlm.nih.gov/Taxonomy/]
ETE: A Python Environment for Tree Exploration
This is a programming library to analyze, manipulate and visualize phylogenetic trees
Ref.A daily-updated tree of (sequenced) life
{{DEFAULTSORT:Phylogenetic Tree Phylogenetics Trees (data structures)