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12 Publications visible to you, out of a total of 12
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence

Abstract

Not specified

Authors: Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz Von Looz, Antonis Rokas

Date Published: 29th Aug 2019

Publication Type: Journal

Error-Profile-Aware Correction of Next Generation Sequencing Read

Abstract

Not specified

Author: Sarah Lutteropp

Date Published: 2017

Publication Type: Master's Thesis

Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

Abstract

Not specified

Authors: Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas

Date Published: 2017

Publication Type: Journal

Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo

Abstract

Not specified

Authors: P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, T. Flouri

Date Published: 2016

Publication Type: Journal

Two Independent and Highly Efficient Open Source TKF91 Implementations

Abstract (Expand)

In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized … open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in 1991. This paper has two parts. In the educational part, we cover teaching issues regarding the setup of the course and the practical and summarize student and teacher experiences. In the scientific part, the two student teams (Team I: Nikolai, Sebastian, Daniel; Team II: Sarah, Pierre) present their solutions for implementing efficient and numerically stable implementations of the TKF91 algorithm. The two teams worked independently on implementing the same algorithm. Hence, since the implementations yield identical results -with slight numerical deviations- we are confident that the implementations are correct. We describe the optimizations applied and make them available as open-source codes in the hope that our findings and software will be useful to the community as well as for similar programming practicals at other universities.

Authors: Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomas Flouri, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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