ALE pipeline

ALE specifications


Unique identifier OMICS_14973
Name ALE
Alternative name Amalgamated likelihood estimation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A dated binary species tree, a set of conditional clade probabilities obtained from a Markov Chain Monte Carlo sample of gene tree topologies.
Output data The reconciled gene trees.
Operating system Unix/Linux
Programming languages C++
License Other
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Gergely Szöllősi <>

Publication for Amalgamated likelihood estimation

ALE IN pipeline

PMCID: 5635595
PMID: 26537223
DOI: 10.1093/gbe/evv204

[…] mukul bansal for advice on maximally parsimonious reconciliation algorithms as well as access to the most current version of dtl-ranger package, and gergely szollosi for consultation regarding amalgamated likelihood estimation and its implementation. they also thank paweł krajewski for preliminary, critical reading of the manuscript. they declare that no conflict of interest […]

ALE institution(s)
Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, Villeurbanne, France; Université de Lyon, Lyon, France; ELTE-MTA “Lendület” Biophysics Research Group, Budapest, Hungary; Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Pozńan, Poland; Université Claude Bernard Lyon 1, UMR CNRS 5558 - LBBE, Lyon, France; Department of Integrative Biology, University of California, Berkeley, CA, USA; Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, Montbonnot, France
ALE funding source(s)
This work was supported by the Marie Curie Fellowship 253642 “Geneforest” and the Albert Szent-Györgyi Call-Home Researcher Scholarship A1-SZGYA-FOK-13-0005, by a Human Frontier Science Program fellowship, and by the French Agence Nationale de la Recherche (ANR) through Grant (ANR-10-BINF-01-01) “Ancestrome”.

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