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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- A. Stamatakis
- 21 January 2014
This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
- A. Stamatakis
- Computer ScienceBioinform.
- 1 October 2006
UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
A rapid bootstrap algorithm for the RAxML Web servers.
This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
ARB: a software environment for sequence data.
The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
This paper presents the latest release of the program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor.
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
The PEAR software for merging raw Illumina paired-end reads from target fragments of varying length evaluates all possible paired- end read overlaps and does not require the target fragment size as input, and implements a statistical test for minimizing false-positive results.
A general species delimitation method with applications to phylogenetic placements
- Jiajie Zhang, P. Kapli, P. Pavlidis, A. Stamatakis
- Biology, Environmental ScienceBioinform.
- 29 August 2013
The Poisson tree processes (PTP) model is introduced to infer putative species boundaries on a given phylogenetic input tree and yields more accurate results than de novo species delimitation methods.
Phylogenomics resolves the timing and pattern of insect evolution
The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Phylogenetic models of rate heterogeneity: a high performance computing perspective
- A. Stamatakis
- Biology, Computer ScienceProceedings 20th IEEE International Parallel…
- 25 April 2006
The intention of this paper is to show that - from a purely empirical point of view - CAT can be used instead of Gamma, the main advantage of CAT over Gamma consists in significantly lower memory consumption and faster inference times.
Selecting optimal partitioning schemes for phylogenomic datasets
- R. Lanfear, B. Calcott, D. Kainer, C. Mayer, A. Stamatakis
- Biology, Computer ScienceBMC Evolutionary Biology
- 17 April 2014
These two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets are developed: strict and relaxed hierarchical clustering, which provide the best current approaches to inferring partitions on very large datasets.