Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2405.16346

A modular and scalable web platform for computational phylogenetics

Nyckollas Brandão·André Jesus·André Páscoa·Alexandre P. Francisco·Mário Ramirez·Cátia Vaz
View original source ↗Read source document ↗Export metadata ↓

Abstract

Phylogenetic analysis, which allow to understand the evolution of bacterial and viral epidemics, requires large quantities of data to be analysed and processed for knowledge extraction. One of the major challenges consists on the integration of the results from typing and phylogenetic inference methods with epidemiological data, namely in what concerns their integrated and simultaneous analysis and visualization. Numerous approaches to support phylogenetic analysis have been proposed, varying from standalone tools to integrative web applications that include tools and/or algorithms for executing the common analysis tasks for this kind of data. However, most of them lack the capacity to integrate epidemiological data. Others provide the ability for visualizing and analyzing such data, allowing the integration of epidemiological data but they do not scale for large data analysis and visualization. Namely, most of them run inference and/or visualization optimization tasks on the client side, which becomes often unfeasible for large amounts of data, usually implying transferring data from existing databases in order to be analysed. Moreover, the results and optimizations are not stored for reuse. We propose the PHYLOViZ Web Platform, a cloud based tool for phylogenetic analysis, that not only unifies the features of both existing versions of PHYLOViZ, but also supports structured and customized workflows for executing data processing and analyses tasks, and promotes the reproducibility of previous phylogenetic analyses. This platform supports large scale analyses by relying on a workflow system that enables the distribution of parallel computations on cloud and HPC environments. Moreover, it has a modular architecture, allowing easy integration of new methods and tools, as well as customized workflows, making it flexible and extensible.

Explore related subjects

q-bio.PEcs.SI

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Nyckollas Brandão, André Jesus, André Páscoa, Alexandre P. Francisco, Mário Ramirez, Cátia Vaz. 2024-05-25. A modular and scalable web platform for computational phylogenetics. https://arxiv.org/abs/2405.16346

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Mutation Order and Selection Shape Intratumor Heterogeneity in Tumor Evolution

Cancer progression often requires multiple driver mutations, but the same drivers may be acquired in different orders. How these pathways jointly shape tumor clonal structure remains unclear. We develop a multitype branching-process model in which malignant transformation requires two driver mutations, distinguishing malignant cells by mutation order and the independent transformation event that founded their clone. Under a successive exponential approximation, we establish point-process limits for pathway-specific clone sizes and derive a closed-form expression for the limiting expected Simpson's index of the combined malignant population. When both mutation orders yield malignant cells with the same net growth rate, the index decomposes into effective pathway weights, determined by mutation rates and birth-death dynamics at preceding stages, and within-pathway concentration terms, determined by intermediate-to-malignant growth-rate ratios. A driver's effect on heterogeneity thus depends critically on when it is acquired. A strong driver acquired early expands the intermediate lineage and increases the supply of independent malignant founders, whereas the same driver acquired last strengthens the growth and age advantage of early-founded malignant clones. Under additive fitness effects, these opposing mechanisms can produce a non-monotone relationship between selective advantage and clonal concentration. Threshold-like non-additive fitness effects can generate highly concentrated malignant populations, while order-dependent terminal fitness causes the faster-growing pathway to dominate asymptotically. These results show how mutation order, mutational accessibility, selection, and epistasis jointly determine lineage-level intratumor heterogeneity.

q-bio.PE↗
arXiv2026

Phase transitions in microbial lineage trees

Microbial populations exhibit high cell-to-cell variability, which fundamentally shapes population behavior. A striking consequence is the existence of phase transitions, where small genetic or environmental changes trigger abrupt shifts in population dynamics. While biological phase transitions have often been proposed, connecting observed behavior to the underlying physics has remained challenging. We combine population genetics with statistical physics to show how phase transitions arise naturally in microbial populations. We highlight the existence of a first-order transition in a model of bacterial plasmid engineering and find a strict lower bound on the number of plasmids that can be stably maintained in a population.

q-bio.PE↗
arXiv2026

Phylogenetic Inference and the Stickiness of Fréchet Means, via Precise Asymptotics of an Embedded Random Walk

A well-known phenomenon in statistical analyses of populations of phylogenetic trees in the Billera-Holmes-Vogtmann space is that the topology of the Fréchet mean tree can contain multifurcations (i.e., internal nodes with more than two children), which raises the practical question of whether this reflects a population-level branching structure (hard polytomy) or merely sampling variability in the data (soft polytomy). This is an instance of the more general phenomenon of "stickiness" in non-Euclidean statistics, whereby the sample Fréchet mean in certain non-positively curved stratified spaces becomes permanently trapped in a lower-dimensional stratum. In this work, we identify a particular multidimensional random walk embedded within the Fréchet mean process, and we show that the time at which stickiness occurs is determined by the largest last-passage time above zero of the coordinates of this random walk. Using this representation, we develop a fully nonparametric procedure for estimating the probability that trifurcations in a sample Fréchet mean tree will bifurcate at some future time if more observations are collected. Lastly, we apply our methodology to a problem in phylogenetics where we consider whether an observed trifurcation in the species tree of primates, glires, and tree shrews is genuinely trifurcated at the population level.

q-bio.PE↗