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One approach could be to implement model partitioning by inferring among-site variation from the alignment, for example, using a mixture model in the context of a Bayesian framework, such as that developed by Lartillot and Philippe (2004) in PhyloBayes, where each site in the alignment falls into one of several classes characterized by its own set of frequencies (CAT model).
Our goal is to infer among-individual variation in navigation ability.
The shared evolutionary history of these bacterial strains is evidenced by the large number of homologues inferred among predicted open reading frames (ORFs) (Figure 3A) and by the number of these that have best or near best hits among these genomes in total genome BLAST searches.
Identification of anchors (or seeds for alignment) for whole-genome comparison plays a fundamental role in comparative genomic analyses because it is required to compute genome-scale multiple alignments [18] [20], and to infer among multiple genomes orthologous genomic segments descendended from the common ancestor without any rearrangement [21].
Phylogenetic relationships inferred among these haplotypes were consistent for both NJ and ML methods.
Three haplotypes of FAE1 can be inferred among these seven B. rapa accessions.
The presence of predicted microsatellite repeat motifs and correspondence of fragment length polymorphism with repeat length expansion/contraction for each polymorphic markers were inferred among chickpea genotypes.
However, the relationships inferred among these seven groups attract substantially less support, dissuading us from combining some but not all of these seven clades to form larger genera.
The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds.
To assess the extent of genetic diversity that can be inferred among human subpopulations by the different arrays, we next compared their FST distributions (Wright 1951).
The major drawback of the BN approach for analyzing gene expression data alone is that the dependencies inferred among variables do not necessarily imply causality.
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