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Andre J. Aberer
Heidelberg Institute for Theoretical Studies
24Publications
15H-index
2,959Citations
Publications 24
Newest
#1Andre J. Aberer (Heidelberg Institute for Theoretical Studies)H-Index: 15
#2Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
Last.Fredrik Ronquist (Swedish Museum of Natural History)H-Index: 44
view all 3 authors...
Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) sampling (for reference implementations, see Lartillot et al. 2009; Drummond et al. 2012; Ronquist et al. 2012) is becoming increasingly popular. One of the most attractive features of the MCMC framework is its ability to handle complex models. The recent introduction of graph-based models (Hohna et al. 2014) will further extend the flexibility of the Bayesian phylogenetic approach. A tree topology with branch lengths is the c...
6 CitationsSource
#1Erich D. Jarvis (HHMI: Howard Hughes Medical Institute)H-Index: 54
#2Siavash Mirarab (University of Texas at Austin)H-Index: 30
Last.Guojie Zhang (UCPH: University of Copenhagen)H-Index: 61
view all 27 authors...
Background: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Findings: Here we present the datasets asso...
41 CitationsSource
#1Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
#2Andre J. Aberer (Heidelberg Institute for Theoretical Studies)H-Index: 15
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers. Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and s...
122 CitationsSource
#1Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
#2Fernando Izquierdo-Carrasco (Heidelberg Institute for Theoretical Studies)H-Index: 7
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 8 authors...
We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implemen...
50 CitationsSource
#1Erich D. Jarvis (HHMI: Howard Hughes Medical Institute)H-Index: 54
#2Siavash Mirarab (University of Texas at Austin)H-Index: 30
Last.Guojie Zhang (UCPH: University of Copenhagen)H-Index: 61
view all 105 authors...
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird sp...
886 CitationsSource
#1Bernhard MisofH-Index: 40
#2Shanlin LiuH-Index: 12
Last.Xin ZhouH-Index: 31
view all 101 authors...
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ord...
1,039 CitationsSource
#1Andre J. Aberer (Heidelberg Institute for Theoretical Studies)H-Index: 15
#2Kassian Kobert (Heidelberg Institute for Theoretical Studies)H-Index: 7
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size. Our software introduces a nonblocking parallelization of Metropolis-coupled chains, modifications for efficient analyses of data sets comprising thousands of partitions and memory saving techniques. We report on...
174 CitationsSource
Sep 8, 2014 in WABI (Workshop on Algorithms in Bioinformatics)
#1Kassian Kobert (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 4 authors...
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function we address the problem of distributing divisible items to a given number of bins. The task is to balance the overall sum of (fractional) item sizes per bin, while keeping the maximum number of unique elements in any bin to a minimum. We show that this problem is NP-hard and give a polynomial time approximation algorithm that yields a solution where the sums of (possibly fractional) item sizes are ba...
12 CitationsSource
#1Bernhard MisofH-Index: 40
#2Shanlin LiuH-Index: 12
Last.Xin ZhouH-Index: 31
view all 101 authors...
#1Emiliano Dell'Ampio (University of Vienna)H-Index: 8
#2Karen Meusemann (CSIRO: Commonwealth Scientific and Industrial Research Organisation)H-Index: 21
Last.Bernhard MisofH-Index: 40
view all 15 authors...
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phyloge...
80 CitationsSource
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