Amalgamated likelihood estimation

[…] 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 […]

[…] 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 […]

[…] 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. […]

[…] 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 […]

[…] 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 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 […]