8 documents found, page 1 of 1
Distance-based phylogenetic inference from typing data: a unifying view
Vaz, Cátia; Nascimento, Marta; Carrico, Joao; Rocher, Tatiana; Francisco, Alexandre P.Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. Moreover, their use is becoming standard, in particular with the introduction of high-throughput sequencing. On the other hand, the data being generated are massive and many algorithms have been proposed for a phylogenetic analysis of typing data, addressing both...
Fast phylogenetic inference from typing data
Carrico, Joao; Crochemore, Maxime; Francisco, Alexandre; Pissis, Solon; Gonçalves, Bruno RibeiroBackground: Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequencebased typing methods are a gold standard for epidemiological surveillance due to the inherent portability of sequence and allelic profile data, fast analysis times and their capacity to create common nomenclatures for strains or clones. This led to development of several novel methods and several databa...
Fast phylogenetic inference from typing data
Carrico, Joao; Crochemore, Maxime; Francisco, Alexandre; Pissis, Solon; Ribeiro-Gonçalves, Bruno; Vaz, CátiaBackground: Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of sequence and allelic profle data, fast analysis times and their capacity to create common nomenclatures for strains or clones. This led to development of several novel methods and several databa...
GrapeTree: visualization of core genomic relationships among 100,000 bacterial ...
Zhou, Zhemin; Alikhan, Nabil-Fareed; Sergeant, Martin; Luhmann, Nina; Vaz, Cátia; Francisco, Alexandre; Carrico, Joao; Achtman, MarkCurrent methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct gene...
PHYLOViZ 2.0: providing scalable data integration and visualization for multipl...
Nascimento, Marta; Sousa, Adriano; Ramirez, Mario; Francisco, Alexandre; Carrico, Joao; Vaz, CátiaHigh Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. How...
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, anal...
Ribeiro-Gonçalves, Bruno; Francisco, Alexandre P.; Vaz, Cátia; Ramirez, Mário; Carrico, JoaoHigh-throughput sequencing methods generated allele and single nucleotide polymorphism information for thousands of bacterial strains that are publicly available in online repositories and created the possibility of generating similar information for hundreds to thousands of strains more in a single study. Minimum spanning tree analysis of allelic data offers a scalable and reproducible methodological alternati...
PHYLOViZ: phylogenetic inference and data visualization for sequence based typi...
Francisco, Alexandre P.; Vaz, Cátia; Monteiro, Pedro T.; Melo-Cristino, José; Ramirez, Mario; Carrico, JoaoBackground: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associat...
An ontology and a REST API for sequence based microbial typing data
Almeida, João; Tiple, João; Ramirez, Mário; Melo-Cristino, José; Vaz, Cátia; Francisco, Alexandre P.; Carrico, JoaoIn the Microbial typing field, the need to have a common understanding of the concepts described and the ability to share results within the community is an increasingly important requisite for the continued development of portable and accurate sequence-based typing methods. These methods are used for bacterial strain identification and are fundamental tools in Clinical Microbiology and Bacterial Population Gen...