ALE specifications

Information

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

Download

Versioning

Add your version

Documentation

Issues: https://github.com/ssolo/ALE/issues

Maintainer

Gergely Szöllősi <>

Publication for Amalgamated likelihood estimation

Efficient exploration of the space of reconciled gene trees.

2013 Syst Biol

PMCID: 3797637

PMID: 23925510

DOI: 10.1093/sysbio/syt054

ALE IN pipeline

The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis

2015

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”.

ALE reviews

Be the first to review ALE