TopiaryExplorer protocols

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TopiaryExplorer specifications

Information


Unique identifier OMICS_08829
Name TopiaryExplorer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format Newick
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rob Knight <>

Publication for TopiaryExplorer

TopiaryExplorer in pipeline

2016
PMCID: 5381614
PMID: 27694476
DOI: 10.1093/gbe/evw235

[…] orf concatenates shorter than 3,000 nucleotides were excluded from the rscu analysis. the resulting dendrogram accounted for 2,885 contigs with cumulative length of 27 mb, and was visualized with topiaryexplorer (). a set of 40 contigs with cumulative length of 1.3 mb derived from the cluster of eukaryotic contigs were examined to ensure microsporidian affinity using blastp searches […]


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TopiaryExplorer in publications

 (2)
PMCID: 5381614
PMID: 27694476
DOI: 10.1093/gbe/evw235

[…] orf concatenates shorter than 3,000 nucleotides were excluded from the rscu analysis. the resulting dendrogram accounted for 2,885 contigs with cumulative length of 27 mb, and was visualized with topiaryexplorer (). a set of 40 contigs with cumulative length of 1.3 mb derived from the cluster of eukaryotic contigs were examined to ensure microsporidian affinity using blastp searches […]

PMCID: 3284489
PMID: 22383988
DOI: 10.1371/journal.pone.0031009

[…] mepal, an implementation of placement using an alignment-free generalization to indels of felsenstein's phylogenetic pruning algorithm , now imports and writes out this format as well. the topiaryexplorer tree visualization package is now in the process of being extended to read this format for visualization., this work would not have been possible without an ongoing collaboration […]


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TopiaryExplorer institution(s)
Department of Pharmacology, University of Colorado Denver, Aurora, CO, USA; Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Boulder, CO, USA
TopiaryExplorer funding source(s)
Bill and Melinda Gates Foundation; the National Institutes of Health (DK78669, HG4872 HG4866, 3T15LM009451-03S1); Howard Hughes Medical Institute

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