Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F21%3A10438111" target="_blank" >RIV/00216208:11310/21:10438111 - isvavai.cz</a>
Result on the web
<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=OZ_HuFWfxK" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=OZ_HuFWfxK</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s12859-021-04274-6" target="_blank" >10.1186/s12859-021-04274-6</a>
Alternative languages
Result language
angličtina
Original language name
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life
Original language description
Background Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. Results Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). Conclusion The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.
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
10611 - Plant sciences, botany
Result continuities
Project
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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
BMC Bioinformatics
ISSN
1471-2105
e-ISSN
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Volume of the periodical
22
Issue of the periodical within the volume
1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
13
Pages from-to
355
UT code for WoS article
000671688100001
EID of the result in the Scopus database
2-s2.0-85110010639