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104 Publications visible to you, out of a total of 104
Quantitative Analysis and Characterization of Natural Language Evolution Datasets

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Methods for phylogenetic inference have been developed mainly for the reconstruction of evolutionary relationships of species based on biological sequence data. However, these methods are also made use … of in linguistics for inferring phylogenies concerning the evolution of natural languages. In the scope of this thesis, we examine the corresponding linguistic input data. We conduct a case study on an exemplary morphosyntactic data set, examining various methods to analyze the signal it contains and to eliminate geographical information the data may include. Further, we perform analyses on numerous linguistic data sets collected from various sources and assembled in a database. We compare these data sets to morphological data from biology, considering differences in the behavior of phylogenetic inferences with RAxML-NG. Additionally, we investigate how it impacts the tree inferences, whether we represent a data set by a binary or by a multi-valued MSA. We study how to model subjectivity related with synonym selection in cognate data. We present probabilistic MSAs as a possible solution and show on an example data set that this might be an appropriate approach

Authors: Luise Häuser, Julia Haag, Alexandros Stamatakis

Date Published: 17th Jun 2023

Publication Type: Master's Thesis

Phylourny: Efficiently calculating elimination tournament win probabilities via phylogenetic methods

Abstract

Not specified

Authors: Ben Bettisworth, Alexander I. Jordan, Alexandros Stamatakis

Date Published: 16th May 2023

Publication Type: Journal

Parallel Inference of Phylogenetic Stands with Gentrius

Abstract

Not specified

Authors: Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis

Date Published: 1st May 2023

Publication Type: Proceedings

The power and limitations of species tree-aware phylogenetics

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Abstract Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. …fer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For example, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress. Significance statement Evolutionary trees provide a framework for understanding the history of life and organising biodiversity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.

Authors: Tom A. Williams, Adrian A. Davin, Benoit Morel, Lénárd L. Szánthó, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szöllősi

Date Published: 17th Mar 2023

Publication Type: Journal

Is there a Correlation between the Use of Swearwords and Code Quality in Open Source Code?

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One of the most fundamental unanswered questions that has been bothering mankind during the Anthropocene is whether the use of swearwords in open source code is positively or negatively correlated with … source code quality. To investigate this profound matter we crawled and analysed over 3800 C open source code containing English swearwords and over 7600 C open source code not containing swearwords from GitHub. Subsequently, we quantified the adherence of these two distinct sets of source code to coding standards, which we deploy as a proxy for source code quality via the SoftWipe tool developed in our group. We find that open source code containing swearwords exhibit significantly better code quality than those not containing swearwords under several statistical tests. We hypothesise that the use of swearwords constitutes an indicator of a profound emotional involvement of the programmer with the code and its inherent complexities, thus yielding better code based on a thorough, critical, and dialectic code analysis process.

Authors: Jan Strehmel, Ben Bettisworth, Dimitri Höhler, Alexandros Stamatakis

Date Published: 1st Feb 2023

Publication Type: Bachelor's Thesis

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

Abstract

Not specified

Authors: Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, N. Ezgi Altınışık, Nikolaos Psonis, Natalia Kashuba, Sevgi Yorulmaz, Robert George, Duygu Deniz Kazancı, Damla Kaptan, Kanat Gürün, Kıvılcım Başak Vural, Hasan Can Gemici, Despoina Vassou, Evangelia Daskalaki, Cansu Karamurat, Vendela K. Lagerholm, Ömür Dilek Erdal, Emrah Kırdök, Aurelio Marangoni, Andreas Schachner, Handan Üstündağ, Ramaz Shengelia, Liana Bitadze, Mikheil Elashvili, Eleni Stravopodi, Mihriban Özbaşaran, Güneş Duru, Argyro Nafplioti, C. Brian Rose, Tuğba Gencer, Gareth Darbyshire, Alexander Gavashelishvili, Konstantine Pitskhelauri, Özlem Çevik, Osman Vuruşkan, Nina Kyparissi-Apostolika, Ali Metin Büyükkarakaya, Umay Oğuzhanoğlu, Sevinç Günel, Eugenia Tabakaki, Akper Aliev, Anar Ibrahimov, Vaqif Shadlinski, Adamantios Sampson, Gülşah Merve Kılınç, Çiğdem Atakuman, Alexandros Stamatakis, Nikos Poulakakis, Yılmaz Selim Erdal, Pavlos Pavlidis, Jan Storå, Füsun Özer, Anders Götherström, Mehmet Somel

Date Published: 2023

Publication Type: Journal

Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data

Abstract (Expand)

Abstract Motivation Missing data and incomplete lineage sorting (ILS) are two major obstacles to accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID have been developed …y methods such as ASTRAL and ASTRID have been developed to account for ILS. However, they can be severely affected by high levels of missing data. Results We present Asteroid, a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is substantially more accurate than ASTRAL and ASTRID for very high proportions (>80%) of missing data. Asteroid is several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. It offers advanced features such as parallelization, support value computation and support for multi-copy and multifurcating gene trees. Availability and implementation Asteroid is freely available at https://github.com/BenoitMorel/Asteroid. Supplementary information Supplementary data are available at Bioinformatics online.

Authors: Benoit Morel, Tom A Williams, Alexandros Stamatakis

Date Published: 2023

Publication Type: Journal

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