Related papers: A format for phylogenetic placements

Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…

Stemmatology is a subfield of philology where one approach to understand the copy-history of textual variants of a text (witnesses of a tradition) is to generate an evolutionary tree. Computational methods are partly shared between the…

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…

Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…

A consensus is emerging that continuous (or metric) measures can be useful in phylogenetic systematics. Many of the methods for coding such characters, how- ever, employ elements that are arbitrary and therefore should be excluded from use…

We present methods to serialize and deserialize tree ensembles that optimize inference latency when models are not already loaded into memory. This arises whenever models are larger than memory, but also systematically when models are…

1.) Spatio-temporal datasets that are difficult to analyze are common in ecological surveys. There are software packages available to analyze these datasets, but many of them require advanced coding skills. There is a growing need for easy…

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…

In this paper we introduce Shackleton as a generalized framework enabling the application of linear genetic programming -- a technique under the umbrella of evolutionary algorithms -- to a variety of use cases. We also explore here a novel…

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…

PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…

Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…

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…

The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…

We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other…