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SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny

Christopher Monit, Richard A Goldstein, Janet Kelso
<span title="2018-02-28">2018</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;
SubRecon calculates the joint probability of states at adjacent internal nodes in a phylogeny, i.e. how the state has changed along a branch.  ...  Existing ancestral sequence reconstruction techniques are ill-suited to investigating substitutions on a single branch of interest.  ...  We present a convenient implementation, SubRecon, which performs this reconstruction for amino acid states.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty101">doi:10.1093/bioinformatics/bty101</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29506148">pmid:29506148</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6022634/">pmcid:PMC6022634</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4ctfhuh74zel3nkggur23zfacy">fatcat:4ctfhuh74zel3nkggur23zfacy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222184403/http://pdfs.semanticscholar.org/3b48/4ef261e5c6b6da89e9a8471b8c867e50b051.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/3b/48/3b484ef261e5c6b6da89e9a8471b8c867e50b051.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty101"> <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/PMC6022634" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

Kristina Straub, Mona Linde, Cosimo Kropp, Samuel Blanquart, Patrick Babinger, Rainer Merkl
<span title="2019-01-09">2019</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/23vvpvouu5bmxknyzbqj2bi4hm" style="color: black;">Biological chemistry</a> </i> &nbsp;
For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool.  ...  The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction  ...  pr48fu by the Leibniz Supercomputing Center of the Bavarian Academy of Sciences and Humanities (LRZ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/hsz-2018-0344">doi:10.1515/hsz-2018-0344</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30763032">pmid:30763032</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wfwa642nyzfq7fy3mg4xky4tgu">fatcat:wfwa642nyzfq7fy3mg4xky4tgu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200309165932/https://hal.inria.fr/hal-02284913/file/FitSS4ASR_V2.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/26/24/262493dd18a180af759a4bee9ba323254c4d4016.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/hsz-2018-0344"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> degruyter.com </button> </a>