Homoplasyfinder

Author: wfry

August undefined, 2024

Web10 feb. 2024 · Author summary Burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic to Southeast Asia and northern Australia. The evaluation of diversity within B. pseudomallei has largely been conducted utilizing clinical isolates despite almost all infections emerging from environmental exposure. In this study, we surveyed … Web1 sep. 2024 · Therefore, to further assess the detection of homoplasies, we applied HomoplasyFinder to the two datasets comprising the same 348 strains (GISAID and SRA) (Table S6). We detected 19 homoplasies on the dataset originating from the SRA, and 21 on the dataset originating from GISAID assemblies. Of these, 19 were detected in both …

HomoplasyFinder: A simple tool to identify homoplasies on a …

Web21 mei 2024 · Homoplasy_ratios.R. In the filtered phylogeny (tree file), for each filtered node of the phylogeny annotated by HomoplasyFinder as corresponding to an ancestor that … uk navy number of ships

SNPPar: identifying convergent evolution and other ... - bioRxiv

WebHere we present HomoplasyFinder, a tool that can be used within the statistical programming environment R and as a Java application. Within R and Java, … Web21 jan. 2024 · Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and … WebR/homoplasyFinder.R defines the following functions: addInconsistentPositionAlignment addScaleBar getMaxCoordinates getTipSequences addInternalNodeLabels … uk navy commander salary range

Frontiers Increased Frequency of Indels in Hypervariable Regions …

Java/Tree.java at master · JosephCrispell/Java · GitHub

Web21 jan. 2024 · Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and … WebHomoplasies were detected on phylogeny using HomoplasyFinder (Crispell, Balaz, and Gordon 2024). We collected all the Omicron sequences from Mexico and used two … ukncryptWeb30 aug. 2024 · Homoplasies, likely signatures of positive selection, were identified using HomoplasyFinder 48. IS6110 insertions in the ppe38 gene locus were screened in the 731 genomes by a specific pipeline, ... uk navy helicopters

"Web14 dec. 2024 · HomoplasyFinder identified 64 (7.65%) homoplasic positions among the generated sequences , mostly located within PE/PPE family proteins, intragenic regions or the pks12 gene (data not shown). A similar proportion (6.70–7.45%) of homoplasies was identified in the alignments obtained from all of the evaluated pipelines. The ... " - Homoplasyfinder

Homoplasyfinder

Java/Tree.java at master · JosephCrispell/Java · GitHub

Web10 jun. 2024 · Topological data analysis identi es emerging adaptive mutations in SARS-CoV-2 Michael Bleher2†*, Lukas Hahn2†*, Juan Angel Patino-Galindo~ 3, Mathieu Carri ere4, Ulrich Bauer5, Raul Rabad an3, Andreas Ott1,2†* 1Mathematics Department, Karlsruhe Institute of Technology, Karlsruhe, Germany 2Mathematical Institute, … Web5 feb. 2024 · HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny: Joseph Crispell · Daniel Balaz · Stephen Vincent Gordon: Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

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Web6 mei 2024 · Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2024 and spread globally to cause the COVID-19 pandemic. Despite the constant accumulation of genetic variation in the SARS-CoV-2 population, there was little evidence for the emergence of significantly more transmissible lineages in the first half of 2024. … WebHomoplasyFinder: a simple tool to identify homoplasies on a phylogeny (PDF) HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny Vincent …

Web2 dec. 2024 · 1. Introduction. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2024 (COVID-19), emerged at the end of 2024 in the province of Wuhan, China, and rapidly spread to other countries, causing more than 5.2 million deaths worldwide as of 18 November 2024 (Platto, Xue, … WebThe results from HomoplasyFinder (consistency index or CI) indicate that NSP1 deletions are among the potential recurrent events in SARS-CoV-2 evolution (Figure 4B and Supplementary Table S1). NSP1 (Δ79-89) was reported to induce lower IFN-I response in the infected Calu-3 cells ( Lin et al., 2024 ), highlighting the biological importance of …

Web7 jun. 2024 · A data.frame object produced by reading in the homoplasyFinder output file produced by runHomoplasyFinderInJava or runHomoplasyFinderJarTool fastaFile The … WebJava / HomoplasyFinder / src / homoplasyFinder / Tree.java Go to file Go to file T; Go to line L; Copy path Copy permalink; This commit does not belong to any branch on this …

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Web21 jan. 2024 · Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and … uk navy service recordsWebWithin R and Java, HomoplasyFinder is shown to be able to automatically, and quickly, identify any homoplasies present in simulated and real phylogenetic data. HomoplasyFinder can easily be incorporated into existing analysis pipelines, either within or outside of R, allowing the user to quickly identify homoplasies to inform downstream … thomas waliser ob gynWeb21 jan. 2024 · Firstly, what is a homoplasy? It is a trait (for example, a nucleotide at a position in an alignment) that is shared between tips that their immediate common … uk navy records ww2