Distance-based phylogenetic inference from typing data: a unifying view

Cátia Vaz; Marta Nascimento; João A. Carriço; Tatiana Rocher; Alexandre P. Francisco

doi:10.1093/bib/bbaa147

Home/Archive/arXiv

arXiv · 2006.07016

Distance-based phylogenetic inference from typing data: a unifying view

Cátia Vaz·Marta Nascimento·João A. Carriço·Tatiana Rocher·Alexandre P. Francisco

View original source ↗Read source document ↗Export metadata ↓

Abstract

Typing 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, addressing both correctness and scalability issues. Most of the distance-based algorithms for inferring phylogenetic trees follow the closest-pair joining scheme. This is one of the approaches used in hierarchical clustering. And although phylogenetic inference algorithms may seem rather different, the main difference among them resides on how one defines cluster proximity and on which optimization criterion is used. Both cluster proximity and optimization criteria rely often on a model of evolution. In this work we review, and we provide an unified view of these algorithms. This is an important step not only to better understand such algorithms, but also to identify possible computational bottlenecks and improvements, important to deal with large data sets.

Explore related subjects

cs.DS q-bio.PE

Keep this discovery

BibTeX RIS

Cátia Vaz, Marta Nascimento, João A. Carriço, Tatiana Rocher, Alexandre P. Francisco. 2020-06-12. Distance-based phylogenetic inference from typing data: a unifying view. https://doi.org/10.1093/bib/bbaa147

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

KEEP EXPLORING

Related papers

arXiv2026

Quasi-Monte Carlo Beyond Hardy-Krause II: $(1 + \varepsilon)n$ Samples Suffice

Numerical integration studies how well one can estimate the integral of a function $f$ over $[0,1)^d$ using $n$ sample points. The two classical methods, Monte Carlo (MC) and quasi-Monte Carlo (QMC), have complementary strengths and weaknesses, and a fundamental question is to design an approach that combines the benefits of both. Recently, building on the transference principle in discrepancy theory, Bansal and Jiang~\cite{BJ25a} gave a randomized QMC method that bridges MC and QMC guarantees using only i.i.d.\ samples. Their method also goes beyond the classical Koksma--Hlawka inequality: it achieves integration error $\widetilde{O}_d(\sigma_{\mathsf{SO}}(f)/n)$, where the smoothed-out variation $\sigma_{\mathsf{SO}}(f)$ can be substantially smaller than the Hardy--Krause variation that governs the classical bound. However, their algorithm requires $n^2$ i.i.d.\ samples as input, and this quadratic blowup is inherent to any method based on the transference principle. In this work, we bypass the quadratic blowup: for any constant $\varepsilon > 0$, we show that $(1+\varepsilon)n$ i.i.d.\ samples suffice to both obtain the beyond-Hardy--Krause guarantee of~\cite{BJ25a}, resolving an open problem posed there, and to produce low-discrepancy point sequences. Our algorithms are variants of the online Haar-thinning method of Dwivedi, Feldheim, Gurel-Gurevich, and Ramdas~\cite{DFG+19}.

cs.DS↗

arXiv2026

A deterministic $(1+\varepsilon)^n$ approximation for the permanent of a nonnegative matrix

For every fixed $0<\varepsilon\le1$, we give a deterministic strongly polynomial algorithm that, given a nonnegative matrix $A\in\mathbb{R}_{\ge0}^{n\times n}$, returns $Q$ satisfying $\operatorname{per} A\le Q\le(1+\varepsilon)^n\operatorname{per} A$.

cs.DS↗

arXiv2026

Single-Exponential Algorithms and a Polynomial Kernel for Strong Connectivity Augmentation

Strong Connectivity Augmentation (SCA) asks whether a directed acyclic graph can be made strongly connected by adding at most $k$ prescribed links whose total weight is within a given budget. Klinkby, Misra, and Saurabh (SODA 2021) gave an $O^*(2^{O(k\log k)})$-time algorithm and asked whether the problem admits a single-exponential parameterized algorithm and a polynomial kernel. We answer both questions affirmatively: SCA can be solved in $O^*(9^k)$ time and admits a polynomial kernel with $O(k^4)$ vertices and $O(k^{16})$ bits. For unweighted SCA, we obtain $O^*(4^k)$ time and a kernel with $O(k^3)$ vertices. Our algorithms are based on a particularly simple reduction to Strongly Connected Spanning Subgraph with two edge costs.

cs.DS↗