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ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa

descriptionPublicationkeyboard_double_arrow_right Article 06 Aug 2018Publisher:Zenodo
Authors: INOUE, Jun;

doi: 10.5281/zenodo.3547154 , 10.5281/zenodo.3490346 , 10.5281/zenodo.1327267 , 10.5281/zenodo.2553737 , 10.5281/zenodo.1452077 , 10.5281/zenodo.1327268

ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa

Abstract

Web tool: We developed a web tool named ORTHOSCOPE to identify orthogroups of specific molecules within major bilaterian lineages. ORTHOSCOPE allows users to employ several sequences of a specific molecule and a user-specified species tree as queries. A test analysis using data from 36 bilaterians was accomplished within 140 seconds. ORTHOSCOPE is freely available at https://github.com/jun-inoue/orthoscope (last accessed 2 October 2019). Data: ORTHOSCOPE employs a genome-scale protein-coding gene database (coding and amino acid sequence datasets) constructed for each species. In order to count numbers of orthologs in each species, only the longest sequence is used when transcript variants exist for single locus. Data versions: 20 Nov. 2019. orthoscopeDB102_20191119.tar.gz 16 Oct. 2019. orthoscopeDB102b.tar.gz 31 Jan. 2019. orthoscopeDB102.tar.gz XX Aug. 2018. orthoscopeDB1a.tar.gz

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Keywords

ORTHOSCOPE, orthogroup, orthology, gene tree, species tree, bilaterians.

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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