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Topic: Dendrogram

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	[No title] (Site not responding. Last check: 2007-10-04)
		The system for displaying a dendrogram may have a function of replacing the subtree selected by the input means with an icon, and a function of restoring the subtree icon to the original subtree in the dendrogram format.
		The system for displaying a dendrogram may have a function of counting and displaying the number of biopolymers containing in their biopolymer information a keyword from a keyword dictionary file, and/or a function of displaying a location of a biopolymer in the dendrogram, which includes the designated keyword.
		A system for displaying a dendrogram according to any one of claims 8 to 10, wherein the system comprises a function of replacing the subtree selected by the input means with an icon, and a function of restoring the subtree icon to the original subtree in the dendrogram format.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=01/45026.010621&ELEMENT_SET=DECL (5935 words)

	Dendrogram in PPI (Site not responding. Last check: 2007-10-04)
		The dendrogram, then, reflects the varying degrees of similarity between the domains/ligands and more distant relationships among groups of closely related domains/ligands.
		Dendrograms are useful to quickly estimate the number of clusters in the data and identify clearly separable clusters and outliers.
		Each node of a dendrogram has a value assigned to it that can be viewed in a pop-up label.
	cfgenomics.unc.edu /genomax3/docs/PPI/Dendrogram_in_PPI.htm (307 words)

	[No title]
		Long vertical lines at the top of the dendrogram indicate that the groups represented by those lines are well separated from one another.
		{p 4 8 2} {cmd:vertlabels} indicates that the labeling for the observations at the bottom of the dendrogram is to be presented vertically instead of horizontally.
		This is helpful when the labels have several characters and there are enough observations in the dendrogram to cause the labels to overlap.
	www.stata.com /updates3/ado/cluster_dendrogram.hlp (926 words)

	Printing a Long Dendrogram
		First, display your dendrogram, moving the similarity cursor to an appropriate postion to indicate clusters.
		Modify the Height parameter to a size that you estimate to be large enough to fit the entire dendrogram.
		Your dendrogram is now ready for printing on a continuous feed printer.
	www.infometrix.com /support/dendrogram.html (459 words)

	Systematics - EvoWiki (Site not responding. Last check: 2007-10-04)
		The overall goal of any method in systematics is to find the dendrogram that best accounts for the data and that presumably reflects the pattern of descent within a clade.
		Criterion-based methods are those that calculate a statistic for each given dendrogram, and then attempt to find that dendrogram with the most extreme value of that statistic.
		In the case of parsimony-based methods, the criterion is the number of 'steps', or character-state changes, and the objective is to minimize this value, i.e., to find the tree with the fewest number of steps.
	wiki.cotch.net /index.php/Systematics (351 words)

	gtree - Draw a tree dendrogram
		Draw a tree dendrogram from PROC CLUSTER/VARLCUS output
		It uses PROC GPLOT to draw the tree dendrogram of the clustering solution.
		PROC TREE does not produce an output dataset suitable for drawing a high=resolution graphic dendrogram.
	www.math.yorku.ca /SCS/sasmac/gtree.html (487 words)

	United States Patent Application: 0040142325
		The method of claim 1, wherein the hierarchy of interest is selected from the group consisting of a tissue expression hierarchy, a developmental expression hierarchy, a pathological expression hierarchy, a cellular expression hierarchy, an intracellular expression hierarchy, a taxonomical hierarchy and a functional hierarchy.
		The method of claim 12, wherein the hierarchy of interest is selected from the group consisting of a tissue expression hierarchy, a developmental expression hierarchy, a pathological expression hierarchy, a cellular expression hierarchy, an intracellular expression hierarchy, a taxonomical hierarchy and a functional hierarchy.
		As used herein a "dendrogram" refers to a branching diagram containing multiple nodes and representing a hierarchy of categories based on degree of similarity or number of shared characteristics.
	appft1.uspto.gov /netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=/netahtml/PTO/srchnum.html&r=1&f=G&l=50&s1="20040142325".PGNR.&OS=DN/20040142325&RS=DN/20040142325 (13898 words)

	EGCG eclustalw
		Having calculated a dendrogram between a set of sequences, the final multiple alignment is carried out by a series of alignments of larger and larger groups of sequences.
		The number of sequences in the dendrogram file must be the same as the number of sequences in the current sequence data set.
		The dendrograms that are produced can only show the relationships between the sequences approximately because the similarity scores are calculated from separate pairwise alignments, not from a multiple alignment (that is what you eventually hope to produce).
	cmgm.stanford.edu /EGCGdoc/source/eclustalw.html (3731 words)

	dendrogram (Statistics Toolbox)
		A dendrogram consists of many U-shaped lines connecting objects in a hierarchical tree.
		generates a dendrogram and returns the permutation vector of the node labels of the leaves of the dendrogram.
		This output indicates that leaf node 20 in the dendrogram contains the original data points 20, 49, 62, 65, 73, and 96.
	www-rohan.sdsu.edu /doc/matlab/toolbox/stats/dendrogram.html (256 words)

	CMSC838b Project: Gene Expression Profile Analysis
		The dendrogram is so wide that even a data sample cannot be displayed in a pixel on a high resolution computer screen.
		In general, dendrogram is usually displayed with a color mosaic at the leaf to show the visual pattern of underlying data.
		Because this direct manipulation instantly updates the actual dendrogram visualizations, users can easily find the color mapping which is most appropriate to reveal the pattern in color mosaic image.
	www.cs.umd.edu /class/spring2001/cmsc838b/Project/Lee_Seo (2485 words)

	ClustalV (Site not responding. Last check: 2007-10-04)
		This dendrogram is used as a guide to align bigger and bigger groups of sequences during the multiple alignment.
		The dendrogram is calculated in 2 stages: 1) all pairs of sequence are compared using the fast/approximate method of Wilbur and Lipman (1983); the result of each comparison is a similarity score.
		Before leaving the dendrogram format, the other 3 columns of numbers are: a pointer to the row from which the "1" sequences were last joined (or zero if only one of them); a pointer to the row in which the "2"s were last joined; the total number of sequences joined in this line.
	www.infobiogen.fr /docs/ClustalW/clustalv.html (7971 words)

	MMU - Biol. Sic., MSc Multivariate Stastics: dendrograms (Site not responding. Last check: 2007-10-04)
		Understanding how a dendrogram is constructed, and how it should be interpreted, is one of the most important aspects of cluster analysis.
		The calculations, and resultant dendrogram, would change with a different distance measure and/or clustering algorithm.
		It appears, from this dendrogram, that the data can be represented by 2 clusters (A and B).
	obelia.jde.aca.mmu.ac.uk /multivar/dend.htm (432 words)

	[No title]
		In a next dialog box, non-exactly matching branches can be dealt with by allowing relative penalties (in percentage) to be set for entries present in the branch of the first tree but not in the branch of the second tree, and vice versa.
		While comparing two dendrograms resulting from different techniques, this tool will facilitate the interpretation and comparison of both dendrograms, by rearranging the branches of the current dendrogram so that the order of entries approaches the order of entries in the other dendrogram as closely as possible.
		After execution of the script, the entries of the chosen branch are selected (blue arrows), and the dendrogram of the other experiment is displayed, with the closest matching branch selected.
	www.applied-maths.com /bn/scripts/comparisons/bncompscripts.htm (1533 words)

	R: Reorder a dendrogram (Site not responding. Last check: 2007-10-04)
		There are many different orderings of a dendrogram that are consistent with the structure imposed.
		This function takes a dendrogram and a vector of values and reorders the dendrogram in the order of the supplied vector, maintaining the constraints on the dendrogram.
		Afterward, at each node, the branches are ordered in increasing weights (where the weight of a branch is defined as the sum of the weights of its sub branches).
	www.oulu.fi /atkk/tkpalv/unix/R/library/stats/html/reorder.html (142 words)

	Stata help for cluster_dendrogram
		Dendrograms graphically present the information concerning which observations are grouped together at various levels of (dis)similarity.
		quick switches to a different style of dendrogram where the vertical lines only go straight up from the observations, instead of the default action of recentering the lines after each merge of observations in the dendrogram hierarchy.
		labels(varname) indicates that varname is to be used in place of observation numbers for labeling the observations at the bottom of the dendrogram.
	www.stata.com /help.cgi?cluster_dendrogram (620 words)

	Mathematical Model for the Construction of Cladograms. 9/25/2005.
		A phenogram is any dendrogram which has been calculated from data about the taxonomic units according to a computer algorithm.
		This dissertation demonstrates that any dendrogram generated by the appropriate phenogram algorithm is a true cladogram, and that this cladogram is unique.
		The phenogram algorithm which emerges as the best (that is, the unweighted pair-group method of Sokal and Michener (1958)) is guaranteed to arrive at the correct solution after a relatively small, finite number of steps.
	www.autopsydb.org /mathclad.htm (4916 words)

	SGD Help: PSI-BLAST Results
		dendrogram is generated by ClustalW with all representative sequences that are hits in the UniRef90 dataset.
		A thumbnail of the dendrogram illustrating the similarity of the sequences is displayed on the left.
		dendrogram is generated by ClustalW using the selected sequences only if the Align All Sequences alignment preference was chosen.
	www.yeastgenome.org /help/SeqSimQuery.html (1560 words)

	SPIDER: CL HC (CLassification - Hierarchical Clustering) (Site not responding. Last check: 2007-10-04)
		This number must be taken from the RESULTS file from the previous run and must be in the range of the scaling of the dendrogram tree.
		The threshold is a scaled value from 0 to 1 that informs 'CL HC' how far "up" the dendrogram you wish it to look.
		A threshold set at the bottem would result in the number of classes being equal to the number of input images.
	www.wadsworth.org /spider_doc/spider/docs/man/clhc.html (365 words)

	Computational Statistics: Hierarchical Clustering
		This inequality is satisfied, for instance, if the data points are leaves of a dendrogram drawing, with the distance defined to be the height of their least common ancestor; in fact this is just an equivalent way of defining an ultrametric.
		Another common data and noise model for DNA sequence input is the Cavender-Farris model [C78], in which the data parameters consist of an ultrametric (dendrogram with edge lengths) together with a prototype sequence stored at the root of the dendrogram.
		The number of possible different dendrograms with k leaves is (2k-1)!!=1357...(2k-1) since there are 2k-1 ways of adding a kth leaf to a (k-1)-leaf dendrogram, so unless k is very small one can't hope to try them all.
	www.ics.uci.edu /~eppstein/280/tree.html (1613 words)

	Molecular phylogenetic tree. (Site not responding. Last check: 2007-10-04)
		In this section you will plot a dendrogram displaying the measured similarities between the seven proteins which you pairwise aligned in Section 5.
		You will compare there relative position in the dendrogram to their relative position in the phylogenetic tree of life.
		Print out the dendrogram, or copy it down on paper, along with the names of the proteins.
	www.ks.uiuc.edu /Training/SumSchool/bioinformatics/node9.html (417 words)

	PileUp (Site not responding. Last check: 2007-10-04)
		The clustering strategy represented by the dendrogram is called UPGMA that stands for unweighted pair-group method using arithmetic averages (Sneath, P.H.A. and Sokal, R.R. (1973) in Numerical Taxonomy (pp; 230-234), W.H. Freeman and Company, San Francisco, California, USA).
		The dendrogram shows the order of the pairwise alignments of sequences and clusters of sequences that together generate the final alignment.
		The dendrogram is not a phylogenetic reconstruction, although the vertical branch lengths are proportional to the distance between the sequences.
	www.genomics.purdue.edu /gcg/gcg-docs/pileup.html (4896 words)

	MAExplorer - Microarray Exploratory Data Analysis
		Clicking on a region in the dendrogram sets a distance threshold (displayed at the top) and displays all parts of the dendrogram tree in red that have a cluster distance less than what you defined.
		B) Details of clustergram and dendrogram are shown where the user had selected a cluster distance threshold at "Mouse mRNA for mitochondrial cytochrome c oxidase subunit Vb" in the dendrogram part of the plot (zoomed by 2X).
		This selection draws all parts of the dendrogram tree that are less than this distance are drawn in red.
	www.lecb.ncifcrf.gov /MaeRefMan/hmaeDoc2.4.5.html (3657 words)

	R: General Tree Structures (Site not responding. Last check: 2007-10-04)
		The code is still in testing stage and the API may change in the future.
		logical indicating if the dendrogram should be draw horizontally or not.
		The dendrogram is directly represented as a nested list where each component corresponds to a branch of the tree.
	www.oulu.fi /atkk/tkpalv/unix/R/library/stats/html/dendrogram.html (400 words)

	MSV Variation Figures
		Strain level relationships are boxed, as are species level relationships: thus nodes of the dendrogram within one of the two shaded boxes define either strain- or species-level relationships.
		The dendrogram was constructed using a program called NJTREE from data produced as outlined for Fig.
		The sequences were aligned and compared as described (Rybicki and Hughes, 1990), and a dendrogram constructed, rooted on a PanSV sequence (not shown).
	www.mcb.uct.ac.za /msv/msvvariationfigs.htm (641 words)

	SPIDER: CL CLA (CLassification - Clustering)
		The class relationships are represented in the form of a dendrogram (tree structure).
		The lengths of the branches (in horizontal print direction) are proportional to the heirarchy indices.
		Each cutoff point in the dendrogram, from right to left, defines a new classification scheme with the number of classes increasing by 1 each time.
	www.wadsworth.org /spider_doc/spider/docs/man/clcla.html (399 words)

	Data Clustering
		The next figure is an example of a dendrogram.
		The dendrogram will be split in a number of groups, with extra space between the groups.
		It describes the dendrogram in the figure at the top of this document.
	odur.let.rug.nl /~kleiweg/clustering/clustering.html (1247 words)

	[No title]
		A low co-phenetic correlation is an indication that the tested samples do not form any real clusters, and such dendrograms should be interpreted with care.
		A dendrogram is a very rough representation of the data it was created from, and the lower the co-phenetic correlation is, the less representative of the data is the dendrogram.
		If you click on the list, the isolates will be sorted in the same order as the dendrogram (click on the list again, and they will be sorted in the original order).
	www.phplate.se /infofiler/php-exempel.doc (2087 words)

	Dendrogram Tree
		The Dendrogram display represents true multi-object data ?Tree objects such as taxonomy, phylogenetic trees (of DNA sequences or proteins, for instance) and developmental cell lineages.
		The ?Tree and associated ACEDB models guiding dendrogram construction are described at the end of this document (see Models).
		The code acts accordingly, displaying the (first) associated dendrogram tree by default, scrolled to the active box set to the given object (except for ?Tree, which is set to the first leaf).
	www.acedb.org /Software/whelp/Dendrogram.html (4803 words)

	SDL Delphi Component Suite - Dendrogram
		The unit DENDROGRAM performs a hierarchical cluster analysis and displays the result as a dendrogram.
		The unit DENDROGRAM is part of the SDL Component Suite.
		This example application generates two clusters of random numbers and displays the results of the cluster analysis as a dendrogram.
	www.lohninger.com /dendrogram.html (162 words)

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