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Topic: Phylogenetic tree

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	29+ Evidences for Macroevolution: Phylogenetics
		Phylogenetics is the scientific discipline concerned with describing and reconstructing the patterns of genetic relationships among species and among higher taxa.
		cladogram: A hierarchical classification of taxa represented as a tree.
		Edwards, A. and Cavalli-Sforza, L. (1964) "Reconstruction of phylogenetic trees." in Phenetic and Phylogenetic Classification.
	www.talkorigins.org /faqs/comdesc/phylo.html (5163 words)

	The PhyloCode: Glossary
		A clade originating from a particular branch (internode) on a phylogenetic tree; a clade encompassing a particular branch on a phylogenetic tree and all nodes and branches descended from that branch; a clade whose name is defined using a branch-based definition.
		A point or vertex on a tree (graph theory); on a phylogenetic tree, a node is commonly used to represent the split of one lineage to form two or more lineages (internal node) or the lineage at the present time (terminal node).
		A clade originating from a particular node on a phylogenetic tree; a clade encompassing a particular node on a phylogenetic tree and all branches (internodes) and nodes descended from that node; a clade whose name is defined using a node-based definition.
	www.ohiou.edu /phylocode/glossary.html (2379 words)

	Tree of Life Web Project
		The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world.
		Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.
		Tree of Life design, images, and icons copyright © 1995-2005 Tree of Life Web Project.
	tolweb.org /tree/phylogeny.html (215 words)

	cars - Phylogenetic tree
		A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor.
		A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree.
		The phylogenetic tree of a single gene or protein taken from a group of species often differs from similar trees for the same group of species, and therefore great care is needed in inferring phylogenetic relationships amongst species.
	www.carluvers.com /cars/Phylogenetic_tree (379 words)

	Phylogenetics Summary
		The taxonomic theory of phylogenetic systematics is organized around the principles that organisms are related through descent from a common ancestor, that there are natural groups of monophyletic taxa, and that unique changes or modifications shared by members of a taxon are evidence of their evolutionary history.
		Phylogenetic relationships among taxa are examined using various kinds of data, including information on the comparative anatomy of fossil species (and of higher taxa), and the anatomy, biochemistry, behavior, and ecology of living organisms.
		Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.
	www.bookrags.com /Phylogenetics (5612 words)

	Phylogenetic tree - InformationBlast
		A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree.
		An unrooted phylogenetic tree is, loosely speaking, a tree derived from a rooted phylogenetic tree by omitting the root.
		The phylogenetic tree of a single gene or protein taken from a group of species often differs from similar trees for the same group of species, and therefore great care is needed in inferring phylogenetic relationships amongst species.
	www.informationblast.com /Phylogenetic_tree.html (335 words)

	DNA BASER - OFFICIAL PAGE. An affordable alternative to the really expensive software for DNA assembly and alignment on ... (Site not responding. Last check: )
		A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor.
		A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree.
		While unrooted phylogenetic trees can be generated from rooted ones by omitting the root from a rooted tree, a root cannot be inferred on an unrooted tree without either an outgroup or additional assumptions (for instance, about relative rates of divergence).
	www.dnabaser.com /articles/phylogenetic-tree/index.html (618 words)

	Phylogenetic Inference
		Using parsimony, phylogenetic tree construction is a search among possible arrangements of relationships among taxa and characters that result in the fewest possible transitions of character states.
		A phylogenetic tree is a branching path from a single point at which all of the character states are ancestral to several points where they are the same as the taxa in the ingroup.
		Constructing the phylogenetic tree involves adding postulated ancestors for each of the unique inclusive/exclusive characters, linking the ancestors together and to the taxa in the ingroup, adding the transitions for the characters which support the structure, and then distributing the homoplasious (conflicting) characters either as parallel gains or gains with subsequent reversals.
	bcrc.bio.umass.edu /ilip/phylinf.html (1500 words)

	Tree of Life Glossary
		This is in contrast to a polytomous tree.
		This is in contrast to a dichotomous tree.
		The root of a subtree of the Tree of Life is the branch that connects the subtree to the remainder of the Tree of Life.
	tolweb.org /tree/home.pages/glossary.html (6244 words)

	29+ Evidences for Macroevolution: Part 1
		However, as illustrated in Figure 1, the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants.
		Since the standard phylogenetic tree is the best approximation of the true historical phylogeny, we expect that all fossilized animals should conform to the standard phylogenetic tree within the error of our scientific methods.
		As mentioned earlier, most phylogenetic trees have some branches with high confidence, because they are well-supported by the data, and other branches in which we have less confidence, because they are statistically less significant and poorly supported by the data.
	www.talkorigins.org /faqs/comdesc/section1.html (12350 words)

	Phylogenetic Tree — Plone CMS: Open Source Content Management (Site not responding. Last check: )
		PhylogeneticTree draws "evolutionary tree" diagrams for representing the evolutionary history of a group of organisms.
		A phylogenetic tree is basically a graph, so perhaps someone could find use for modifying it to show network diagrams and such, although the data input format is likely highly specific to the task at hand, and is thus very simple.
		The method of actually drawing the tree (or graph, should other branching relationships be treated) on graph paper and simple tabulating the row and column position of the nodes is really easy, and even for complicated graphs it should be easy to get a nice plot.
	plone.org /products/phylogenetictree (953 words)

	BioMed Central \| Full text \| Phylogenetic tree information aids supervised learning for predicting protein-protein ...
		One type of data used for prediction is the phylogenetic profile of a protein –; a string of ones and zeros encoding respectively the presence and absence of the protein in a group of genomes, conserved operons, gene fusions, etc. [3-6].
		Instead of comparing two trees directly, which is a highly nontrivial task in terms of both algorithmic implementation and biological interpretation, the mirror tree method uses as a surrogate the distance matrices that store the genetic distance between the protein and its orthologs in a group of genomes.
		The number of clusters is equal to the number of branches at the section, and is determined by the tree and the height where the section is cut – the higher the cut is, the fewer the number of clusters is. For example, in Figure 3, section1 generates 4 clusters: α, β, γ and δ.
	www.biomedcentral.com /1471-2105/8/6 (5759 words)

	Phylogenetic tree of P-type ATPases (Site not responding. Last check: )
		The phylogenetic is based on core sequences from 159 P-type ATPase sequences present in the EMBL and SWISS-PROT databases July 1, 1997.
		The tree was constructed with the Phylip program package using the Protdist and Fitch programmes.
		Some areas (which are not connected to the rest of the tree) have been enlarged 40 % to clarify the distribution of species.
	www.patbase.kvl.dk /tree.html (199 words)

	The reasons for building a phylogenetic tree are as diverse as the methods used to produce the trees
		The reasons for building a phylogenetic tree are as diverse as the methods used to produce the trees.
		Trees derived by way of a character-based method have been optimized according to the distribution of actual data patterns in relation to a specified character.
		Phylogenetic inference methods are under continual evaluation and improvement upon the accuracy and speed of computation in these methods is a continual process.
	bioinfo.mbb.yale.edu /mbb452a/projects/Patricia-M-Strickler.html (1954 words)

	Phylogenetic Tree Terminology (Site not responding. Last check: )
		Phylogenetic trees are designed to reveal evolutionary relationships among DNA or protein sequences.
		The use of the term "tree" has given rise to arborial terminology to describe the different parts of the overall tree.
		Since the visual display of the unrooted tree is very different, it might be beneficial to choose an unrooted tree to depcit clusters of related sequences.
	www.bio.davidson.edu /courses/genomics/seq/treeparts.html (175 words)

	- A Critique of ''29 Evidences for Macroevolution'' - Part 1 -
		The tree that is presented is chosen from a forest of alternatives, typically on the assumption of maximum parsimony.
		It is then alleged that the fossils conform to this expectation, and thus “conform to the standard phylogenetic tree,” in that “intermediates” have been found between reptiles and birds (citing mainly dromaeosaurids) and between reptiles and mammals (citing synapsids) but not between mammals and birds.
		Nonconformity to the standard phylogenetic tree is having traits that are definitive of two taxa that are shown on the phylogeny as having arisen independently of each other (e.g., birds and mammals).
	www.trueorigin.org /theobald1b.asp (8121 words)

	Phylogeny and reconstructing phylogenetic trees
		Any tree can be displayed in two dimensions so that the lines don't cross, and so these phylogenetic trees are.
		It is completely arbitrary whether a branch of the tree is placed to the left or to the right of a dot.
		So, a tree with two species, 1 and 2, with a common ancestor 3, could be drawn with either species 1 or species 2 on the left, and the other species on the right.
	aleph0.clarku.edu /~djoyce/java/Phyltree/intro.html (691 words)

	MB451 Tree construction lecture
		A phylogenetic tree is a representation of the evolutionary/geneological relationships between a collection of organisms (or molecular sequences).
		Trees with a time scale are based on some form of physical data, such as a fossil record, that provide dating information.
		The scales (time) in these two trees are horizontal rather than vertical, and the braches are simple diagonal lines connecting nodes, but the information in these trees is the same as in the previous tree.
	www.mbio.ncsu.edu /MB451/lecture/trees/lecture.html (2135 words)

	Deep Time Project (Site not responding. Last check: )
		Phylogenetic relationships for all the main lineages of vascular plants from Pryer et al.
		Phylogenetic relationships for all the main lineages of vascular plants inferred from a maximum-likelihood (ML) analysis of four combined data sets: chloroplast rbcL, atpB, rps4 and nuclear small-subunit rDNA.
		Molecular phylogenetic analysis shows that the order Charales (stoneworts) is the closest living relatives of land plants, with the Coleochaetales sister to the land plant/Charales lineage.
	www.flmnh.ufl.edu /deeptime/phylogenetictrees.html (307 words)

	Constructing a Phylogenetic Tree
		When the construction of the tree is finished, each person from the original group should represent one present-day organism (at the very tip of a branch).
		Now that you've finished your group¹s Phylogenetic Tree, exchange your group¹s DNA sequences with another group, and, working/thinking "backward" from what you just did, construct in the chart below their phylogenetic tree and label it, as you did yours, with the numbers on the back of their sequences.
		If they approve of your phylogenetic interpretation of their DNA sequences, have a member of that group sign your work and then go on to answer the questions.
	www.accessexcellence.org /AE/AEPC/WWC/1995/simulation_tree.html (1360 words)

	MRC Myosin Home Page
		The full alignment used to produce this tree is published on these pages in plain text form, with secondary structural elements on the chicken pectoralis muscle myosin II subfragment I structure identified[1] and shown above the alignment.
		An unrooted phylogenetic tree is presented, based on a similar tree published elsewhere (Hodge and Cope, 2000), derived from an alignment of 143 members of the myosin superfamily.
		It is immediately apparent that although the sequence region used for the analysis is confined to the motor domain in the myosin head, the classification of the myosins is almost exclusively consistent with that expected from examination of the tail regions, ie those thought to be responsible for interaction with the 'cargo' transported.
	www.mrc-lmb.cam.ac.uk /myosin/trees/trees.html (1184 words)

	Phylogenetic tree (Site not responding. Last check: )
		Building of probable phylogenetic trees is bases on the matrix of pair distances between sequences.
		The algorithm is aimed at construction of the tree, for which this number is minimal, i.e the maximum topological similarity tree.
		This property of cluster trees allows to introduce the distance from the root to each node and to draw the tree using this distance as a node abscissa.
	www.genebee.msu.su /services/hlp/phtree-hlp.html (816 words)

	HIV Database Tree Tutorial
		First of all, it is important to realize that all tree building methods assume that the alignment is correct; errors in the alignment can lead to a very misleading tree.
		The better way is to use the tree you get from the Consense program as input for another run of the tree-building program to have the branch lengths estimated for that particular tree.
		Contrary to what many people think, this is not a test of how accurate your tree is; it only gives information about the stability of the tree topology (the branching order), and it helps assess whether the sequence data is adequate to validate the topology.
	www.hiv.lanl.gov /content/hiv-db/TREE_TUTORIAL/Tree-tutorial.html (2538 words)

	Phylogenetic Tree Tool Reference :: Phylogenetic Analysis (Bioinformatics Toolbox)
		A phylogenetic tree is initially created by pairing the two most similar sequences and then adding the remaining sequences in a decreasing order of similarity.
		Your tree might contain leaves that are far outside the phylogeny, or it might have duplicate leaves that you want to remove.
		Phylogenetic trees can have thousands of leaves and branches, and finding a specific node can be difficult.
	www.mathworks.com /access/helpdesk/help/toolbox/bioinfo/ug/a1072802492b1.html (2139 words)

	HIV Database Tree Tutorial
		First of all, it is important to realize that all tree building methods assume that the alignment is correct; errors in the alignment can lead to a very misleading tree.
		The better way is to use the tree you get from the Consense program as input for another run of the tree-building program to have the branch lengths estimated for that particular tree.
		Contrary to what many people think, this is not a test of how accurate your tree is; it only gives information about the stability of the tree topology (the branching order), and it helps assess whether the sequence data is adequate to validate the topology.
	hiv-web.lanl.gov /TREE_TUTORIAL/Tree-tutorial.html (2538 words)

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