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Journal ArticleDOI

TreeView : an application to display phylogenetic trees on personal computers

01 Aug 1996-Bioinformatics (Oxford University Press)-Vol. 12, Iss: 4, pp 357-358
TL;DR: TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists.
Abstract: TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.

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Citations
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Journal ArticleDOI
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Abstract: Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein— and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

25,931 citations


Cites methods from "TreeView : an application to displa..."

  • ...Consensus trees are written with both branch lengths and posterior clade probabilities, for easy graphical representation using software such as TreeView ( Page, 1996 )....

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  • ...Consensus trees are written with both branch lengths and posterior clade probabilities, for easy graphical representation using software such as TreeView (Page, 1996)....

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Journal ArticleDOI
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Abstract: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

10,773 citations


Cites background or methods from "TreeView : an application to displa..."

  • ...See Goldman, Anderson, and Rodrigo (2000) for a critical review of those methods....

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  • ...The trees with branch lengths calculated from PAML programs should be directly readable by TreeView (Page 1996)....

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  • ...Goldman N, Anderson JP, Rodrigo AG....

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  • ...See pages 250-251 in Yang (2006). (Strictly speaking the above description is accurate if fossil calibration is available for the root only but not for any other nodes....

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  • ...I have found it convenient to create the tree file with labels and read the tree using Rod page’s (1996) TreeView to check that the tree and labels are right....

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Journal ArticleDOI
TL;DR: The current version of iTOL v4 introduces four new dataset types, together with numerous new features, and is the first tool which supports direct visualization of Qiime 2 trees and associated annotations.
Abstract: The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.

4,233 citations

Journal ArticleDOI
TL;DR: The Interactive Tree Of Life (ITOL) as mentioned in this paper is an online tool for the display, manipulation and annotation of phylogenetic and other trees, which allows users to draw shapes, labels and other features directly onto the trees.
Abstract: The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users.

2,856 citations

Journal ArticleDOI
TL;DR: An r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees, which can read more tree file formats than other softwares, and support visualization of phylo, multiphylo, phylo4, phyla4d, obkdata and phyloseq tree objects defined in other r packages.
Abstract: Summary We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

2,692 citations


Cites methods from "TreeView : an application to displa..."

  • ...There aremany software packages and Web tools that are designed for displaying phylogenetic trees, such as TREEVIEW (Page 1996), FIGTREE (Rambaut 2014), TREEDYN (Chevenet et al. 2006), ITOL (Letunic & Bork 2011), EVOLVIEW (Zhang et al. 2012) and DENDROSCOPE (Huson & Scornavacca 2012)....

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References
More filters
Journal ArticleDOI
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

63,427 citations


"TreeView : an application to displa..." refers methods in this paper

  • ...TREEVIEW can read tree files produced by the CLUSTAL W (Thompson et al., 1994), COMPONENT (Page, 1993), fastDNAml (Olsen et al., 1994), Hennig86 (Farris, 1988), MacClade (Maddison and Maddison, 1992), PAUP (Swofford, 1993), PHYLIP (Felsenstein, 1993), the Ribosomal Database Project (Maidak et al.,…...

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  • ...TREEVIEW is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two commonest personal computers used by biologists....

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Book
01 Jan 2005
TL;DR: MacClade is a computer program that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.
Abstract: MacClade is a computer program, with accompanying manual, that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. Systematists and other evolutionary biologists can use its flexible tools to analyse phylogeny and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.

5,175 citations

Journal ArticleDOI
TL;DR: The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services that include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees.
Abstract: The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment.

1,660 citations


"TreeView : an application to displa..." refers background or methods in this paper

  • ...TREEVIEW can read tree files produced by the CLUSTAL W (Thompson et al., 1994), COMPONENT (Page, 1993), fastDNAml (Olsen et al., 1994), Hennig86 (Farris, 1988), MacClade (Maddison and Maddison, 1992), PAUP (Swofford, 1993), PHYLIP (Felsenstein, 1993), the Ribosomal Database Project (Maidak et al., 1994), among others....

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  • ..., 1994), Hennig86 (Farris, 1988), MacClade (Maddison and Maddison, 1992), PAUP (Swofford, 1993), PHYLIP (Felsenstein, 1993), the Ribosomal Database Project (Maidak et al., 1994), among others....

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  • ...…files produced by the CLUSTAL W (Thompson et al., 1994), COMPONENT (Page, 1993), fastDNAml (Olsen et al., 1994), Hennig86 (Farris, 1988), MacClade (Maddison and Maddison, 1992), PAUP (Swofford, 1993), PHYLIP (Felsenstein, 1993), the Ribosomal Database Project (Maidak et al., 1994), among others....

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Journal ArticleDOI
TL;DR: A new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences, which is based on version 3.3 of Felsenstein's dnaml program and significantly improve performance and reduce memory usage, making it feasible to construct even very large trees.
Abstract: We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.

1,117 citations


"TreeView : an application to displa..." refers methods in this paper

  • ...Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers....

    [...]

  • ...TREEVIEW can read tree files produced by the CLUSTAL W (Thompson et al., 1994), COMPONENT (Page, 1993), fastDNAml (Olsen et al., 1994), Hennig86 (Farris, 1988), MacClade (Maddison and Maddison, 1992), PAUP (Swofford, 1993), PHYLIP (Felsenstein, 1993), the Ribosomal Database Project (Maidak et al.,…...

    [...]

  • ...TREEVIEW is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two commonest personal computers used by biologists....

    [...]