Exact(5)
We also found that anterior expression patterns were quicker to evolve sequences than posterior patterns.
These parameters were used to evolve sequences for each of 10,500 genes for each taxon using the Jukes-Cantor model of evolutionary change, allowing nucleotide substitution but not indels.
The ability to estimate parameters of sequence evolution with realistic models, and then computationally evolve sequences using these fitted parameters is crucial to better characterize the behavior of reconstruction methods in realistic settings.
We used the PEBCRES simulation framework (He et al. 2012; Duque et al. 2014) (fig. 1 A and B) to evolve sequences that drive a predetermined expression pattern, simulating the process of evolutionary adaptation under a variety of scenarios.
This set of probe sequences was designated as the ancestral sequence and, along with a phylogenetic tree specifying the relationships and genetic distances among the taxa, was input into the sequence evolution program ROSE v1.3 to evolve sequences for related taxa [ 51].
Similar(55)
Fast evolving sequences, such as those of the planarian S. mediterranea, were not included in this analysis (for the entire dataset, see Additional file 1: Figure S1).
Fast evolving sequences, such as those of the planarian S. mediterranea, were not included in these analyses (for the entire dataset, see Additional files 4, 5: Figure S4, S5).
As part of the Mohr Visiting Artist Program, Henke is working with several Stanford students to perform a digital "music machine". The currently untitled project combines math, music and engineering in randomly evolving sequences of sound.
A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.
None of these evolved sequences had significant linear sequence homology with each other or with Rho-CRE.
TEs also tend to be among the most lineage-specific, i.e. recently evolved, sequences in the human genome [45].
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