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ExaML specifications


Unique identifier OMICS_08024
Name ExaML
Alternative name Exascale Maximum Likelihood
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Parallelization MPI
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes




No version available



  • person_outline Alexandros Stamatakis

Publication for Exascale Maximum Likelihood

ExaML citations


Genes for de novo biosynthesis of omega 3 polyunsaturated fatty acids are widespread in animals

Sci Adv
PMCID: 5931762
PMID: 29732410
DOI: 10.1126/sciadv.aar6849

[…] ted by IsoSVM (892) were then aligned with MAFFT v.7.309 (reference, parameters: --genafpair --maxiterate 1000), and 100 bootstrap maximum likelihood (ML)–based phylogenetic trees were inferred using ExaML tool v.3.0.18 (). The ExaML trees were inferred given 100 precomputed starting trees using standard RAxML v.8.2.9 () following the ExaML manual instructions (https://github.com/stamatak/ExaML/bl […]


Molecular Epidemiology of HIV 1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control

PMCID: 5913615
PMID: 29506269
DOI: 10.1093/infdis/jiy044
call_split See protocol

[…] Phylogenetic trees were estimated by maximum likelihood using ExaML and the R package big.phylo with a general time reversible model of nucleotide substitution and gamma distribution for rate heterogeneity among sites []. One hundred trees were reconstructed fro […]


Step wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

Sci Rep
PMCID: 5816663
PMID: 29453332
DOI: 10.1038/s41598-018-19996-6

[…] For all matrices (M1-M6) an optimal maximum likelihood tree was obtained in the program ExaML version 3.0.1. Models of amino acid substitution were selected using the AUTOF command in ExaML. Node supports were estimated with 300 replicates generated and analyzed with the program RAxML an […]


The State of Software for Evolutionary Biology

Mol Biol Evol
PMCID: 5913673
PMID: 29385525
DOI: 10.1093/molbev/msy014

[…] the pipeline increases dramatically with the number of components. Here, we refer to bugs that do not lead to crashes which are easily detected and fixed, but to bugs that yield incorrect results. In ExaML (), for instance, we detected two major bugs in branch length scaling and bootstrap replicate generation under specific settings while conducting large-scale inferences on empirical data. Thus, […]


HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Evol Bioinform Online
PMCID: 5768271
PMID: 29348708
DOI: 10.1177/1176934317742613

[…] r8. There are several options: ASTRAL, ASTRID (both coalescent summary methods), MRL (supertree method using matrix representation with likelihood), and maximum likelihood implemented in FastTree and ExaML (concatenation). In preparation of an ExaML run, the selected loci are concatenated, and gene partition information is provided by AMAS. Partition Finder 2, is used to find the optimal partition […]


Evaluating Fast Maximum Likelihood Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

Mol Biol Evol
PMCID: 5850867
PMID: 29177474
DOI: 10.1093/molbev/msx302
call_split See protocol

[…] etic analyses on Vanderbilt University’s ACCRE cluster (http://www.accre.vanderbilt.edu/) using the same type of computing nodes. Similarly, a subset of supermatrices were selected and re-analyzed by ExaML v3.0.17, RAxML-PTHREADS v8.2.0, IQ-TREE-OMP v1.4.2, and FastTreeMP v2.1.9 (each with three replicates) on the same type of ACCRE nodes.Likelihood: With respect to likelihood score maximization, […]


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ExaML institution(s)
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and Department of informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
ExaML funding source(s)
All three authors are funded by institutional funds from the Heidelberg Institute for Theoretical Studies for theoretical studies.

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