Profiling phylogenetic informativeness
WebApr 11, 2024 · Gibberellic Acid-Stimulated Arabidopsis (GASA) proteins are present in various plants and have a role in plant growth, stress responses, and hormone crosstalk. GASA coding sequences in barley were discovered in this study. We then investigated gene and protein structure, physicochemical characteristics, evolutionary and phylogenetic … WebNov 1, 2015 · Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used …
Profiling phylogenetic informativeness
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WebAug 8, 2014 · We evaluate phylogenetic informativeness (PI) profiles [ 36] for gene sequences sampled among major actinopterygian lineages and demonstrate that is not … WebFeb 1, 2024 · We used phylogenetic informativeness profiling, maximum likelihood and coalescent-based phylogenetic analyses, measures of barcode utility, and genealogical sorting indices to assess the performance of the several molecular markers used in Colletotrichum systematics and taxonomy across all known species complexes. While …
WebTally Approximations of Phylogenetic Informativeness Rapidly (TAPIR) - 1.0 - a Python package on PyPI - Libraries.io. ... Townsend JP: Profiling phylogenetic informativeness. Systematic Biol. 2007, 56:222-231. Pond SLK, Frost SDW, Muse SV: HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679. WebJun 28, 2024 · Phylogenetic informativeness profiles with relatively low and gradual peaks can be seen in 18S and protein-coding genes, including COI, TOPO, and CADMC. Regarding rRNA genes, the highest net PI is obtained for 28S, followed by 16S and 12S, while the slow-evolving 18S gene contains comparatively little information. However, a peak of the PI can …
WebNov 5, 2013 · By studying the evolutionary properties of the markers we sequenced, profiling their phylogenetic informativeness (sensu Townsend [ 27 ]) under different alignment procedures, and comparing inferred topologies, we predict their utility for phylogenetic inference at shallower and deeper taxonomic levels. Materials and Methods 1. Taxonomic … WebApr 1, 2014 · Markers were targeted to maximize phylogenetic informativeness and to exclude multi-copy genes. We demonstrate the universality of these markers by testing a portion of them on a taxonomically diverse assemblage of avian specimens. ... López-Giráldez F, Townsend JP (2011) PhyDesign: an online application for profiling …
WebAug 6, 2012 · Phylogeographic research exploded in popularity and now serves as an important bridge between phylogenetics and population genetics, promoting conceptual advances that straddle the boundary between these disciplines (e.g., species trees and related approaches to species delimitation).
WebNov 30, 2024 · Their flexibility and biological sensibility make them appealing for many phylogenetic comparative applications. Previously available packages placed … extended stay hotels near tucker gaWebOct 24, 2024 · The phylogenetic analyses in this study inferred the Alternaria section classification for all isolates but was unable to infer species identities for all isolates. This was likely caused by a lack of available Alternaria reference sequences for all three loci and other loci of phylogenetic informativeness (Lawrence et al. 2013; Raja et al. 2011). buchf 22WebNov 9, 2024 · As phylogenetic profiling is commonly used to understand functional interactions at the pathway level, we compared the different methods at this level. For each pathway, we calculated the... extended stay hotels near ucf