Results 21 to 30 of about 1,369,061 (328)
Tangent Phylogenetic PCA [PDF]
, 2023 Phylogenetic PCA (p-PCA) is a version of PCA for observations that are leaf nodes of a phylogenetic tree. P-PCA accounts for the fact that such observations are not independent, due to shared evolutionary history. The method works on Euclidean data, but in evolutionary biology there is a need for applying it to data on manifolds, particularly shapes ...
Akhøj, Morten +2 more
openaire +4 more sources
Phylogenetic context using phylogenetic outlines [PDF]
, 2021 AbstractMicrobial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes.
Caner Bagci +3 more
openaire +2 more sources
Biovalentia: Biological Research Journal, 2021 Sumatran elephant is a subspecies of endemic Asian elephants on the island of Sumatra and is included in the Red List of the International Union for Conservation of Nature (IUCN) with critically endangered status.
Elsa Virnarenata +4 more
doaj +1 more source
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
bioRxiv, 2019 IQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models ...
B. Minh +6 more
semanticscholar +1 more source
The role of edaphic environment and climate in structuring phylogenetic pattern in seasonally dry tropical plant communities [PDF]
, 2015 This study was made possible through the kind financial support of the São Paulo Research Foundation - http://fapesp.br/en (Fundação de Amparo à Pesquisa do Estado de São Paulo - Fapesp 2013/15280-9).Seasonally dry tropical plant formations (SDTF) are ...
Araújo, Francisca Soares de +5 more
core +9 more sources
A new species of Charinus Simon 1892 from Brazil, with notes on behavior (Amblypygi, Charinidae)
ZooKeys, 2016 A new species of Charinus is described and illustrated from the Brazilian Atlantic Forest. Charinus ruschii sp. n. is found in Santa Lúcia reserve, Espírito Santo state, and is sympatric with C. brasilianus and C. montanus.
Gustavo Miranda +4 more
doaj +3 more sources
OrthoFinder: phylogenetic orthology inference for comparative genomics
Genome Biology, 2019 Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative
David M. Emms, S. Kelly
semanticscholar +1 more source
Phylogenetic comparative assembly [PDF]
Algorithms for Molecular Biology, 2009 Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further.
Husemann, Peter, Stoye, Jens
openaire +7 more sources
ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates
Nature Methods, 2017 Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic ...
S. Kalyaanamoorthy +4 more
semanticscholar +1 more source
Integrating influenza antigenic dynamics with molecular evolution
eLife, 2014 Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains ...
Trevor Bedford +9 more
doaj +1 more source