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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

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

[…] 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 […]


The State of Software for Evolutionary Biology

PMCID: 5913673
PMID: 29385525
DOI: 10.1093/molbev/msy014

[…] 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, […]


Italian guidelines on the assessment and management of pediatric head injury in the emergency department

PMCID: 5769508
PMID: 29334996
DOI: 10.1186/s13052-017-0442-0

[…] with head trauma are discharged from the ed, either after initial assessment or following a period of observation:i.gcs 15j.asymptomatic or significant improvement in symptomsk.normal neurological examl.no suspicion of child abusem.reliable caregivers and ability to easily return to the edn.no other injuries requiring admission, gcs 15, asymptomatic or significant improvement in symptoms, […]


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

PMCID: 5850867
PMID: 29177474
DOI: 10.1093/molbev/msx302

[…] the development of programs for fast, yet accurate, inference. for example, several different fast programs have been developed in the very popular maximum likelihood framework, including raxml/examl, phyml, iq-tree, and fasttree. although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far […]


Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination

PMCID: 5629823
PMID: 28992304
DOI: 10.1093/gbe/evx188

[…] and used the single best maximum likelihood tree [ln(likelihood) of − 3,2145,034.7] starting from 15 unique random trees and from 15 unique parsimonious trees, as calculated by raxml v8.2.4 () and examl v3.0 (). this tree included 82 genomes from pneumococcus complex 3 () and 240 pmen-1 genomes (); we excluded these strains from all of our further analyses because they were originally sampled […]


Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

PMCID: 5604124
PMID: 28934378
DOI: 10.1093/gbe/evx168

[…] contain a platypus and seven marsupial families as outgroups, with 92 eutherian species representing 80 families., we performed maximum likelihood (ml) inference on the concatenated data set using examl ver. 3.0.15 () assuming a general time reversible model with γ-distributed rates among sites. we performed 20 ml searches and evaluated node support with 100 bootstrap replicates. bootstrapped […]

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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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