ATV: display and manipulation of annotated phylogenetic

By Christian M. Zmasek, Sean R. Eddy. Bioinform., 2001

309 citations recorded by the source corpus.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e54243445a47ec98322a7ce20ac23ab00f28acd8

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Citations in the corpus

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. (2010, methodology): “Once the execution is finished, the results are sent back to the user via an electronic message, which includes a link to a Web page displaying the estimated tree using the ATV Java applet (Zmasek and Eddy 2001).”
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana (2004, methodology): “Pairs of gene family members falling within a synteny block are annotated as such in the phylogeny, using the extended New Hampshire (NHX) format [84].”
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation (2007, methodology): “Tools like TREEVIEW (Page, 1996), NJPLOT (Perriere and Gouy, 1996), ATV (Zmasek and Eddy, 2001), TaxonTree (Parr et al.”
Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice (2012, methodology): “Based on this information, can manually prune taxa from the input data set, visualize, and subsequently retrieve the pruned result m be r 2018 For visualization, we employ the Archaeopteryx viewer (Zmasek and Eddy 2001).”
Influenza Research Database: An integrated bioinformatics resource for influenza research and surveillance (2012, unknown): “The IRD also provides a customized tree viewer based on Archae-opteryx (http://www.phylosoft.org/archaeopteryx) 42 that incorporates Archaeopteryx functions, such as re-rooting, subtree ordering, and branch swapping in addition to allowing the user to decorate the tree labels based on sequence…”
Recent developments in the MAFFT multiple sequence alignment program (2008, methodology): “Alignments and phylogenetic trees are visualized with the Jalview [96] and ATV [97] viewers, respectively.”
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, unknown): “The protein tree can be can be downloaded as picture or in NH format, and it is possible to edit the tree interactively in the ATV tree viewer (38).”
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses (2010, methodology): “To date, a variety of tree visualization tools have been released, among which ATV [17], Dendroscope [18], FigTree (the tree editor accompanying BEAST), the MEGA tree explorer [19], Mesquite [20], PhyloWidget [21], TreeDyn [22] and TreeView [23] may be the most widely distributed.”
TreeDyn: towards dynamic graphics and annotations for analyses of trees (2006, methodology): “Most popular tools such as Treeview [1] and ATV [9] lay out trees in a two dimensional Euclidean space and are useful for visualising trees of up to a few hundred nodes; PoInTree makes uses of polar coordinates [26].”
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels (2006, background): “In the ‘Phylogenetics’ section, users can view the precomputed neighbor-joining trees for each of the transporter families through an ATV java applet (18).”
phyloXML: XML for evolutionary biology and comparative genomics (2009, methodology): “There are multiple tree-viewing programs that support the format, including Archaeopteryx [13] (the successor to the tree display tool ATV [7]) and TreeViewJ [14].”
TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “alignments; and an extended version of the ATV tree viewer (31) is used to display and edit phylogenetic trees.”
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011, background): “(1) direct display of numeric values above the branches in the tree; (2) display of symbols whose size is proportional to the bootstrap values; and (3) coloring of tree branches using user specified color gradients, with actual colors calculated from the associated bootstrap value.”