Alexandros Stamatakis
Heidelberg Institute for Theoretical Studies
Publications 199
High‐throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long‐read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtai...
#1Dora Serdari (Heidelberg Institute for Theoretical Studies)
#2Evangelia-Georgia Kostaki (UoA: National and Kapodistrian University of Athens)H-Index: 3
Last.Paschalia Kapli (UCL: University College London)H-Index: 12
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#1Paula Breitling (KIT: Karlsruhe Institute of Technology)
#2Ben Bettisworth (Heidelberg Institute for Theoretical Studies)
Last.Alexandros StamatakisH-Index: 50
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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 interc...
#1Nicolas Comte (IRIA: French Institute for Research in Computer Science and Automation)H-Index: 1
#2Benoit MorelH-Index: 5
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Motivation: Gene and species tree reconciliation methods can be used to root gene trees and correct uncertainties that are due to scarcity of signal in coming from phylogenetic methods based uniquely on multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack of performance on certain functions, or usability for biologists. Results: We present Treerecs, a phylogenetic software based on duplication-loss reconciliati...
#1Benoit Morel (Heidelberg Institute for Theoretical Studies)H-Index: 5
#2Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
Last.Gergely J. Szöllősi (MTA: Hungarian Academy of Sciences)H-Index: 18
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Inferring gene trees is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges species tree-aware methods seek to use information from a putative species tree. However, there are few methods available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive da...
#1Umberto Perron (EMBL-EBI: European Bioinformatics Institute)H-Index: 1
#2Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
Last.Iain H Moal (GSK: GlaxoSmithKline)H-Index: 1
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2 CitationsSource
#1Xiaofan Zhou (SCAU: South China Agricultural University)H-Index: 18
#2Sarah Lutteropp (Heidelberg Institute for Theoretical Studies)H-Index: 1
Last.Antonis Rokas (Vandy: Vanderbilt University)H-Index: 55
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#1Sarah Lutteropp (Heidelberg Institute for Theoretical Studies)H-Index: 1
#2Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
Last.Alexandros StamatakisH-Index: 50
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Recently, Lemoine et al. suggested the Transfer Bootstrap Expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support metric on taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Therefore, we developed a fast and memory-efficient TBE implementation. We improved upon the original algorithm described by Lemoine et al. by introducing multiple algorithmic and technical optimizations. On empiri...
1 CitationsSource
#1David Laehnemann (HHU: University of Düsseldorf)H-Index: 1
#2Johannes Köster (University of Duisburg-Essen)H-Index: 13
Last.Alexander Schönhuth (UU: Utrecht University)H-Index: 22
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Background: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut. Novel methods: Here, we present novel an...
4 CitationsSource