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António Pedro Branco, Cátia Vaz and Alexandre P. Francisco
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees. These tools re...
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Jacques Demongeot, Joël Gardes, Christophe Maldivi, Denis Boisset, Kenza Boufama and Imène Touzouti
Background: In present genomes, current relics of a circular RNA appear which could have played a central role as a primitive catalyst of the peptide genesis. Methods: Using a proximity measure to this circular RNA and the distance, a new unsupervised cl...
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Samuel R. Schrader and Eren Gultepe
The evaluation of similarities between natural languages often relies on prior knowledge of the languages being studied. We describe three methods for building phylogenetic trees and clustering languages without the use of language-specific information. ...
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Nawal Abd El-Baky, Neama Mahmoud Fattouh Rezk and Amro A. Amara
This study aimed to map the differences between Arthrospira sp. and Arthrospira platensis strains and variants from the order Oscillatoriales at the gene and protein levels of C-phycocyanin alpha chain via multiple alignment, phylogenetic trees of specie...
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Yunting Zhang, Meiyi Deng, Xianjie Gu, Chenhui Guo, Yan Chen, Yuanxiu Lin, Qing Chen, Yan Wang, Yong Zhang, Ya Luo, Xiaorong Wang and Haoru Tang
Ethylene at least partly regulates some aspects during non-climacteric ripening in strawberry. However, the ethylene signaling pathway genes in the strawberry fruit have not been comprehensively and systematically analyzed. In the present study, 15 FaETR...
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Ruriko Yoshida, Lillian Paul and Peter Nesbitt
Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences. Since we use equidistant trees as ...
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Minhyuk Park, Paul Zaharias and Tandy Warnow
The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate ...
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David Schaller, Manuela Geiß, Marc Hellmuth and Peter F. Stadler
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least resolved trees....
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Brona Brejová and Rastislav Královic
In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps ...
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Filippo Bussotti and Martina Pollastrini
Climate change and extreme drought and heat events impact the Mediterranean evergreen sclerophyllous vegetation in South Europe, especially in Iberian and Italian peninsula, where widespread crown defoliation and dieback have been observed since the 90s ...
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