PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F21%3A43903639" target="_blank" >RIV/60076658:12310/21:43903639 - isvavai.cz</a>
Alternative codes found
RIV/61988987:17310/21:A2202BSX RIV/60077344:_____/21:00555135
Result on the web
<a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001365" target="_blank" >https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001365</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1371/journal.pbio.3001365" target="_blank" >10.1371/journal.pbio.3001365</a>
Alternative languages
Result language
angličtina
Original language name
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Original language description
Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
PLoS Biology
ISSN
1544-9173
e-ISSN
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Volume of the periodical
19
Issue of the periodical within the volume
8
Country of publishing house
US - UNITED STATES
Number of pages
22
Pages from-to
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UT code for WoS article
000685554400001
EID of the result in the Scopus database
2-s2.0-85112130434