POWER, the PhylOgenetic WEb Repeater, is a web-based service designed to perform user-friendly pipeline phylogenetic analysis. POWER uses an open-source LAMP structure and infers genetic distances and phylogenetic relationships using well-established algorithms (ClustalW and PHYLIP). POWER incorporates a novel tree builder based on the GD library to generate a high-quality tree topology according to the calculated result. POWER accepts either raw sequences in FASTA format or user-uploaded alignment output files. Through a user-friendly web interface, users can sketch a tree effortlessly in multiple steps. After a tree has been generated, users can freely set and modify parameters, select tree building algorithms, refine sequence alignments or edit the tree topology. All the information related to input sequences and the processing history is logged and downloadable for the user's reference. Furthermore, iterative tree construction can be performed by adding sequences to, or removing them from, a previously submitted job. POWER is accessible at http://power.nhri.org.tw.
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http://dx.doi.org/10.1093/nar/gki494 | DOI Listing |
BMC Genomics
January 2025
Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
Background: The evolution and development of flowers are biologically essential and of broad interest. Maize and sorghum have similar morphologies and phylogeny while harboring different inflorescence architecture. The difference in flower architecture between these two species is likely due to spatiotemporal gene expression regulation, and they are a good model for researching the evolution of flower development.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Baylor College of Medicine, Houston, TX, USA.
Background: Alzheimer's Disease (AD) incidence is almost double in female than male, suggesting sex-specific AD risk genes remain unknown.
Method: We designed a statistical physics approach that exploits freely available but massive evolutionary and phylogenetic coupling data on sequence variation and speciation. These couplings lead to quantifiable values for the selection pressure exerted on the genes within a population.
New Phytol
January 2025
Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK.
Plants produce floral nectar as a reward for pollinators, which contains carbohydrates and amino acids (AAs). We designed experiments to test whether pollinators could exert selection pressure on the profiles of AAs in nectar. We used HPLC to measure the free AAs and sugars in the nectar of 102 UK plant species.
View Article and Find Full Text PDFMol Phylogenet Evol
December 2024
Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands; Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands. Electronic address:
The ease with which genome-wide data can nowadays be collected allows complicated phylogenetic questions to be re-evaluated. Phylogenetic relationships among newts have often proven difficult to resolve due to the prevalence of incomplete lineage sorting and introgressive hybridization. For the newt genus Lissotriton, phylogenetic relationships are not settled and there is controversy surrounding the species status of several taxa.
View Article and Find Full Text PDFExp Appl Acarol
December 2024
Laboratory of Parasitology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia.
Hyalomma ticks are important vectors of pathogens affecting human and animal health. This study aimed to assess the outputs of three molecular markers (16S, 12S rRNA, and COI) for accurate tick species molecular identification, genetic diversity assessment, and phylogenetic positioning of Hyalomma tick specimens from Tunisia. A total of 20 tickspecimens were collected from different hosts including cattle, camels, and turtles in nine Tunisian governorates.
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