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Renewing Felsenstein's phylogenetic bootstrap in the era of big data

F. Lemoine, J.-B. Domelevo Entfellner, E. Wilkinson, D. Correia, M. Dávila Felipe, T. De Oliveira, O. Gascuel
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
In 1985, Joseph Felsenstein proposed the use of the bootstrap to assess the robustness, or repeatability, of phylogenetic trees 3 .  ...  Here we propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or  ...  big. phylo).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41586-018-0043-0">doi:10.1038/s41586-018-0043-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29670290">pmid:29670290</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jrkg3mj3lbfltcjcilr3kzpa6y">fatcat:jrkg3mj3lbfltcjcilr3kzpa6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200309214442/http://repository.uwc.ac.za/xmlui/bitstream/handle/10566/3673/Lemoine_Renewing-Felstein_2018.pdf;jsessionid=2E4F4BB5F9D1A3183D8F45987FCB4F2A?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/9b/ee9bf9d0b617130fc0c06273cddc1f24d978e5bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41586-018-0043-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases [article]

Berend Snel, Leny M van Wijk
<span title="2020-01-27">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Several phylogenetic trees of the ePK repertoire of single eukaryotes have been published, including the human kinome tree.  ...  The retention of these LECA ePKs in present-day species is highly variable.  ...  proteome dataset and members of the Snel lab for critical reading and helpful discussion on the 37  ... 
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711201337/https://www.biorxiv.org/content/biorxiv/early/2020/01/27/2020.01.27.920793.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f6/89/f6894e1bf0850c5b7dd04045f9424058df92ea77.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.27.920793"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The Thermosynechococcus genus: wide environmental distribution, but a highly conserved genomic core [article]

Alannah Paulina Prondzinsky, Sarah J Berkemer, Lewis M Ward, Shawn E McGlynn
<span title="2020-10-21">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of protein coding genes has implications for understanding the basis of thermophily  ...  Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan.  ...  ., and Gascuel, 448 O. (2018) Renewing Felsenstein's phylogenetic bootstrap in the era of big data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.20.346296">doi:10.1101/2020.10.20.346296</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hsmwb3jrfngxlfrq7aaufy4rja">fatcat:hsmwb3jrfngxlfrq7aaufy4rja</a> </span>
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Quantifying the Adaptive Potential of a Nascent Bacterial Community [article]

Joao A Ascensao, Kelly M Wetmore, Benjamin H Good, Adam P Arkin, Oskar Hallatschek
<span title="2022-02-05">2022</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Tremendous progress has been made in quantifying the strength and abundance of selected mutations available to single microbial species in simple environments, lacking strong ecological interactions.  ...  The background dependence of mutational effects appears to reflect widespread changes in which gene functions are important for determining fitness, for all but the most strongly interacting genes.  ...  Renewing Felsenstein's phylogenetic bootstrap in the era 920 of big data. Nature 2018 556:7702, 556(7702):452-456, 4 2018. ISSN 1476-4687. doi: 921 10.1038/s41586-018-0043-0. 922 54.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.02.03.475969">doi:10.1101/2022.02.03.475969</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ar6xsdxjyjgrzgslsmgmv3kxrm">fatcat:ar6xsdxjyjgrzgslsmgmv3kxrm</a> </span>
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