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List of works by Alexandros Stamatakis

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.

scientific article published on 22 March 2017

A Format for Phylogenetic Placements ⬇️

scientific article published on February 22, 2012

A fast and memory-efficient implementation of the transfer bootstrap

scientific article published on 01 April 2020

A functional phylogenomic view of the seed plants

scientific article

A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences

scientific article

A rapid bootstrap algorithm for the RAxML Web servers

scientific article (publication date: October 2008)

Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty

scientific article published in October 2023

Aligning short reads to reference alignments and trees

scientific article published on 2 June 2011

Assessing the root of bilaterian animals with scalable phylogenomic methods

scientific article

Biggest challenges in bioinformatics

scientific article (publication date: April 2013)

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects

scientific article (publication date: 2014)

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

scientific article published on 01 March 2019

Evolutionary Relationships among Chlamydophila abortus Variant Strains Inferred by rRNA Secondary Structure-Based Phylogeny ⬇️

scientific article published on May 24, 2011

ExaBayes: massively parallel bayesian tree inference for the whole-genome era.

scientific article published on 18 August 2014

ExaML version 3: a tool for phylogenomic analyses on supercomputers

scientific article published on 29 March 2015

GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

scientific article published on 05 June 2020

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

scientific article published on 04 February 2020

Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

scientific article published on 29 November 2019

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

scientific article

Methods for automatic reference trees and multilevel phylogenetic placement

scientific article published on 01 April 2019

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

scientific article published on 01 January 2020

Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States

scientific article published on 01 September 2019

Modelling structural constraints on protein evolution via side-chain conformational states: Supplementary files

NetRAX: accurate and fast maximum likelihood phylogenetic network inference

scientific article published in 2022

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets ⬇️

scientific article published on July 3, 2012

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

scientific article

Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda

scientific article

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes

article

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

article

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood

scientific article

Photoreceptor diversification accompanies the evolution of Anthozoa

scientific article published on 23 November 2020

Phylogenetic analysis of SARS-CoV-2 data is difficult

scientific article published on 15 December 2020

Phylogenomic analyses data of the avian phylogenomics project

scientific article

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences

scientific article published on 4 March 2016

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

scientific article

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

scientific article published on 27 January 2014

Prediction of missing sequences and branch lengths in phylogenomic data

scientific article

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice

scientific article published on 6 September 2012

Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence

scientific article published on 01 March 2020

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

scholarly article published 27 July 2017

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

scientific article (publication date: May 2014)

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

scientific article published on 01 November 2019

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

scientific article (publication date: November 2006)

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.

scientific article published on 21 March 2018

Result verification, code verification and computation of support values in phylogenetics ⬇️

scientific article published on January 21, 2011

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

scientific article published on 29 September 2020

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.

scientific article published on 28 May 2019

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites

scholarly article published 29 April 2016

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

The state of software for evolutionary biology

scientific article published on 29 January 2018

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

scientific article published on 16 July 2020

Understanding angiosperm diversification using small and large phylogenetic trees ⬇️

scientific article published on March 2, 2011

UniEuk: Time to Speak a Common Language in Protistology!

scientific article

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

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