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Protocols

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

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Maintainer


  • person_outline Gergely Szöllősi

Publication for Amalgamated likelihood estimation

ALE citations

 (9)
call_split

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

2017
Nat Commun
PMCID: 5331214
PMID: 28230052
DOI: 10.1038/ncomms14319
call_split See protocol

[…] nces were observed multiple times in a single host, only one sequence was retained in the alignment. Replicate sequences observed in multiple hosts were all conserved in the OTU alignment.We used the ALE algorithm to detect the co-speciation and host-shift events along the phylogenetic tree of 16S sequences. ALE employs a probabilistic and event-based approach, reconciling the symbiont phylogeneti […]

library_books

Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes

2017
BMC Evol Biol
PMCID: 5209957
PMID: 28049420
DOI: 10.1186/s12862-016-0850-6

[…] structing a gene phylogeny taking into account potential events of gene duplication, transfer and loss and tries to draw evolutionary scenarios using a “consensus” species tree as a reference []. The Amalgamated Likelihood Estimation (ALE) method, a gene tree-aware approach based on probabilistic models that include parameters for gene duplication, loss and transfer, was used for tree reconciliati […]

library_books

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

2015
Genome Biol Evol
PMCID: 5635595
PMID: 26537223
DOI: 10.1093/gbe/evv204

[…] ases. Again, majority of splits are well supported by both Bayesian and ML results. Notably, although approximately 15% of splits (60/413) present in the Bayesian consensus tree are challenged during ALE reconciliation, the subdivision into major clades (as depicted on ) is not modified. […]

library_books

Genome scale phylogenetic analysis finds extensive gene transfer among fungi

2015
PMCID: 4571573
PMID: 26323765
DOI: 10.1098/rstb.2014.0335

[…] ch motivated other approaches based on the consideration of a set of candidate gene trees obtained using faster approaches that do not consider a species tree. These approaches include TreefixDTL [], ALE [,] and TERA []. The latter two approaches are extensions of an idea initially proposed in [] and formalized in [] and are particularly fast and accurate. They are based on the ‘amalgamation’ idea […]

library_books

Quantifying MCMC Exploration of Phylogenetic Tree Space

2015
Syst Biol
PMCID: 4395846
PMID: 25631175
DOI: 10.1093/sysbio/syv006

[…] sal distributions in a subset of Markov chains (Metropolis-coupled or otherwise) along with chains using a general proposal distribution. CCD has also begun to see use in phylogenomic methods such as amalgamated likelihood estimation (), which uses CCD directly as a proxy for posterior probability in order to infer a species tree joint with a set of gene trees. Biases in CCD will bias the results […]

call_split

Joint amalgamation of most parsimonious reconciled gene trees

2014
Bioinformatics
PMCID: 4380024
PMID: 25380957
DOI: 10.1093/bioinformatics/btu728
call_split See protocol

[…] joint sequence-reconciliation score. As shown in Figure 1 in the online appendix, amalgamation permits us to explore a vastly larger set of trees than those contained in the sample.Conceptually, both ALE () and TERA are based on the amalgamation approach of AnGST (), and all three methods are—at the level of the dynamic programming recursion—closely related. TERA differs from AnGST in the underlyi […]

Citations

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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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