14 documents found, page 1 of 2
Computing RF tree distance over succinct representations
Branco, António Pedro; Vaz, Cátia; Francisco, Alexandre P.There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees. These tools rely on several inference methods available to produce phylogenetic trees, with resulting trees not being unique. Thus, methods for comparing phylogenies that are...
phyloDB: A framework for large-scale phylogenetic analysis of sequence based ty...
Lourenço, Bruno; Vaz, Cátia; Coimbra, Miguel E.; Francisco, Alexandre P.phyloDB is a modular and extensible framework for large-scale phylogenetic analyses of sequence based typing data, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an API for representing and querying phylogenetic data. Custom algorithms are also supported, allowing users to perform heavy computations directl...
phyloDB: a framework for large-scale phylogenetic analysis of sequence based ty...
Lourenço, Bruno; Vaz, Cátia; Coimbra, Miguel E.; Francisco, Alexandre P.PHYLODB is a modular and extensible framework for large-scale phylogenetic analyses of sequence based typing data, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an API for representing and querying phylogenetic data. Custom algorithms are also supported, allowing users to perform heavy computations directl...
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...
Towards distance-based phylogenetic inference in average-case linear-time
Crochemore, Maxime; Francisco, Alexandre P.; Pissis, Solon; Vaz, CátiaComputing genetic evolution distances among a set of taxa dominates the running time of many phylogenetic inference methods. Most of genetic evolution distance definitions rely, even if indirectly, on computing the pairwise Hamming distance among sequences or profiles. We propose here an average-case linear-time algorithm to compute pairwise Hamming distances among a set of taxa under a given Hamming distance t...
Dynamic phylogenetic inference for sequence-based typing data
Francisco, Alexandre P.; Nascimento, Marta; Vaz, CátiaTyping methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High Throughput Sequencing (HTS). On the other hand, the data being generated is massive and many algorithms have been proposed for phylogenetic analysis of typing data, such as the goeBUR...
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...
NGSPipes: from specification to automatic deployment of NGS pipelines
Dantas, Bruno; Fleitas, Calmenelias; Francisco, Alexandre P.; Simão, José; Vaz, CátiaBiosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the following is true for many areas of science: published results are usually hard to reproduce either because data is not available or tools are not readily available, which de...
NGS4Cloud: Cloud-based NGS Data Processing
Forja, João; Almeida, Alexandre; Francisco, Alexandre P.; Simão, José; Vaz, CátiaMotivation and challenges: Next-Generation Sequencing (NGS) technologies are greatly increasing the amount of genomic computer data, revolutionizing the biosciences field and leading to the development of more complex NGS Data Analysis techniques [2]. These techniques, known as pipelines or workflows, consist of running and refining a series of intertwined computational analysis and visualization tasks on large...
Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) ...
Teixeira, Andreia Sofia; Monteiro, Pedro T.; Carrico, Joao Andre; Ramirez, Mário; Francisco, Alexandre P.Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by int...