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Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M Glover, Gaston H Gonnet, Adrian M Altenhoff, Christophe Dessimoz
<span title="2017-07-12">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.  ...  Results: We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in  ...  Acknowledgements We thank Georgina Bland for her contribution to the refinement for asymmetrically evolving paralogs, and Karina Zile for her thoughtful review of the article.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx229">doi:10.1093/bioinformatics/btx229</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28881964">pmid:28881964</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5870696/">pmcid:PMC5870696</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6nhrdpyjgjhsno5r5uwrosv64q">fatcat:6nhrdpyjgjhsno5r5uwrosv64q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220113425/http://pdfs.semanticscholar.org/22d7/651b60e82b9fce099babfc2f4959794ad7fb.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/22/d7/22d7651b60e82b9fce099babfc2f4959794ad7fb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx229"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870696" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz
<span title="2017-07-15">2017</span>
With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.  ...  Results: We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in  ...  Acknowledgements We thank Georgina Bland for her contribution to the refinement for asymmetrically evolving paralogs, and Karina Zile for her thoughtful review of the article.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3929/ethz-b-000191311">doi:10.3929/ethz-b-000191311</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zcxtq7vn3zcgldredqxcco4dvu">fatcat:zcxtq7vn3zcgldredqxcco4dvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211210184249/https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/191311/btx229.pdf;jsessionid=612C89C4E82035A1FAD2398008F46154?sequence=2" 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/f0/a4/f0a4958fb52f64ebc406bfd18d525e04a8da7f4f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3929/ethz-b-000191311"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Telling the whole story in a 10,000-genome world

Robert G Beiko
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5tyg6kdofe7db2hdtm2zxndi4" style="color: black;">Biology Direct</a> </i> &nbsp;
The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups  ...  Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based  ...  I would also like to thank members of my research group and the Leverhulme Trust Questioning the Tree of Life network for many productive conversations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-6150-6-34">doi:10.1186/1745-6150-6-34</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21714939">pmid:21714939</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3158115/">pmcid:PMC3158115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/izdcredminea7fkz7he7cjp6la">fatcat:izdcredminea7fkz7he7cjp6la</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111114032247/http://www.biology-direct.com/content/pdf/1745-6150-6-34.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/13/44/1344dd7c86f1e574da98e80309c4877d93704f2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-6150-6-34"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158115" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>