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38 Publications visible to you, out of a total of 38
SCRAPP : A tool to assess the diversity of microbial samples from phylogenetic placements

Abstract

Not specified

Authors: Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis

Date Published: 9th Oct 2020

Publication Type: Journal

The windblown: possible explanations for dinophyte DNA in forest soils

Abstract

Not specified

Authors: Marc Gottschling, Lucas Czech, Frédéric Mahé, Sina Adl, Micah Dunthorn

Date Published: 10th Aug 2020

Publication Type: Journal

Petabase-scale sequence alignment catalyses viral discovery

Abstract

Not specified

Authors: Robert C. Edgar, Jeff Taylor, Tomer Altman, Pierre Barbera, Dmitry Meleshko, Victor Lin, Dan Lohr, Gherman Novakovsky, Basem Al-Shayeb, Jillian F. Banfield, Anton Korobeynikov, Rayan Chikhi, Artem Babaian

Date Published: 10th Aug 2020

Publication Type: Journal

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

Abstract

Not specified

Authors: Alexey Kozlov, Joao Alves, Alexandros Stamatakis, David Posada

Date Published: 2nd Aug 2020

Publication Type: Journal

A fast and memory-efficient implementation of the transfer bootstrap

Abstract (Expand)

Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. …. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

Authors: Sarah Lutteropp, Alexey M Kozlov, Alexandros Stamatakis

Date Published: 1st Apr 2020

Publication Type: Journal

RootDigger : a root placement program for phylogenetic trees

Abstract

Not specified

Authors: Ben Bettisworth, Alexandros Stamatakis

Date Published: 14th Feb 2020

Publication Type: Journal

Empirical Analysis of Phylogenetic Quasi-Terraces

Abstract (Expand)

Terraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition … models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.

Authors: Paula Breitling, Alexandros Stamatakis, Olga Chernomor, Ben Bettisworth, Lukasz Reszczynski

Date Published: 18th Oct 2019

Publication Type: Journal

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