Academic Journal
Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets
| العنوان: | Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets |
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| المؤلفون: | Doizy, Anna, Prin, Amaury, Cornu, Guillaume, Chiroleu, Frédéric, Rieux, Adrien |
| المصدر: | Bioinformatics Advances |
| بيانات النشر: | Oxford University Press |
| سنة النشر: | 2023 |
| المجموعة: | CIRAD: Agritrop (Centre de coopération internationale en recherche agronomique pour le développement) |
| مصطلحات موضوعية: | U10 - Informatique, mathématiques et statistiques, F40 - Écologie végétale, phylogénie, évolution, séquence d'adn, méthode statistique, adn, tempête orageuse, http://aims.fao.org/aos/agrovoc/c_13325, http://aims.fao.org/aos/agrovoc/c_2745, http://aims.fao.org/aos/agrovoc/c_27812, http://aims.fao.org/aos/agrovoc/c_7377, http://aims.fao.org/aos/agrovoc/c_2347, http://aims.fao.org/aos/agrovoc/c_14820 |
| الوصف: | Motivation: Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results: To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | text |
| اللغة: | English |
| Relation: | http://agritrop.cirad.fr/607968/; Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets. Doizy Anna, Prin Amaury, Cornu Guillaume, Chiroleu Frédéric, Rieux Adrien. 2023. Bioinformatics Advances, 3 (1):vbad026, 5 p.https://doi.org/10.1093/bioadv/vbad026; http://agritrop.cirad.fr/607968/1/vbad026.pdf |
| DOI: | 10.1093/bioadv/vbad026 |
| الاتاحة: | http://agritrop.cirad.fr/607968/ http://agritrop.cirad.fr/607968/1/vbad026.pdf https://doi.org/10.1093/bioadv/vbad026 |
| Rights: | cc_by ; info:eu-repo/semantics/openAccess ; https://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: | edsbas.BE9911C6 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/bioadv/vbad026 |
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