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Tomáš Flouri
University College London
29Publications
10H-index
1,259Citations
Publications 29
Newest
#1Antonia G. P. Ford (UCL: University College London)H-Index: 3
#2Thomas R. Bullen (UCL: University College London)H-Index: 1
Last.Julia J. Day (UCL: University College London)H-Index: 16
view all 14 authors...
Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlids (commonly referred to as ‘tilapia’), having significant scientific and socioeconomic importance both within and beyond their native range. Unique among cichlids, several species o...
2 CitationsSource
#1Diego Darriba (Heidelberg Institute for Theoretical Studies)H-Index: 9
#2David Posada (University of Vigo)H-Index: 54
Last.Tomáš Flouri (UCL: University College London)H-Index: 10
view all 6 authors...
ModelTest-NG is a re-implementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate, and introduces several new features, such as ascertainment bias correction, mixture and FreeRate models, or the automatic processing of partitioned datasets. ModelTest-NG is available under a GNU GPL3 license at ...
5 CitationsSource
#1Pierre Barbera (Heidelberg Institute for Theoretical Studies)H-Index: 3
#2Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 7 authors...
Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACE...
23 CitationsSource
#1Diep Thi Hoang (University of Engineering and Technology, Lahore)H-Index: 3
#2Le Sy Vinh (University of Engineering and Technology, Lahore)H-Index: 7
Last.Bui Quang Minh (Max F. Perutz Laboratories)H-Index: 18
view all 6 authors...
Background The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony.
11 CitationsSource
#1Tomáš Flouri (UCL: University College London)H-Index: 10
#2Xiyun Jiao (UCL: University College London)H-Index: 1
Last.Ziheng Yang (UCL: University College London)H-Index: 85
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16 CitationsSource
#1Diego Darriba (Heidelberg Institute for Theoretical Studies)H-Index: 9
#2Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analy...
8 CitationsSource
#1Benoit Morel (Heidelberg Institute for Theoretical Studies)H-Index: 5
#2Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
Continuous advances in molecular sequencing technologies now allow for inferring evolutionary trees (phylogenies) on supercomputers that comprise hundreds to thousands of species at the whole-transcriptome or whole-genome level. The phylogenetic likelihood function (PLF) consumes 90-95% of total execution time in such analyses and is therefore typically parallelized. Recently, the site repeats (SR) technique for substantially accelerating the PLF has been introduced. It identifies repeating patt...
2 CitationsSource
#1Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
#2Jiajie Zhang (Heidelberg Institute for Theoretical Studies)H-Index: 8
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 5 authors...
Next-Generation Sequencing (NGS) technologies have reshaped the landscape of life sciences. The massive amount of data generated by NGS is rapidly transforming biological research from traditional wet-lab work into a data- intensive analytical discipline (Koboldt et al., Cell 155(1):27–38, 2013). The Illumina “sequencing by synthesis” technique (Mardis, Annu Rev Genomics Hum Genet 9:387–402, 2008) is one of the most popular and widely used NGS technologies.
Source
Oct 1, 2016 in KSE (Knowledge and Systems Engineering)
#1Diep Thi Hoang (University of Engineering and Technology, Lahore)H-Index: 3
#2Le Sy Vinh (University of Engineering and Technology, Lahore)H-Index: 7
Last.Bui Quang Minh (Max F. Perutz Laboratories)H-Index: 18
view all 6 authors...
Reconstructing maximum parsimony (MP) trees along with bootstrap for large multiple sequence alignments is a computationally challenging task. In this paper, we present MPBoot, a new method for approximating MP bootstrap based on the idea of a previously introduced method for maximum likelihood bootstrap. MPBoot economizes the computations by only sampling trees on the original alignment and simultaneously calculating exact parsimony scores for all bootstrap alignments. Preliminary experiments o...
Source
#1David Dao (KIT: Karlsruhe Institute of Technology)H-Index: 1
#2Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
Our ability to infer large phylogenetic trees that contain up to tens of thousands of species, gives rise to novel challenges in computational phylogenetics. Phylogenetic accuracy decreases as we add more and more taxa while keeping the number of sites in an alignment fixed. In addition, it is difficult, if not impossible to visually inspect such large phylogenies in order to determine whether they “make sense” or not. So, how can we assess the biological plausibility of a huge phylogeny? Here, ...
1 CitationsSource
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