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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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Documentation
Maintainer
- person_outline Gergely Szöllősi
Publication for Amalgamated likelihood estimation
ALE citations
(9)Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
[…] 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 […]
Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes
[…] 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 […]
The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis
[…] 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. […]
Genome scale phylogenetic analysis finds extensive gene transfer among fungi
[…] 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 […]
Quantifying MCMC Exploration of Phylogenetic Tree Space
[…] 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 […]
Joint amalgamation of most parsimonious reconciled gene trees
[…] 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 […]
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