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The MADL framework is capable of generating two types of cycle accurate simulators, one based on the dynamic-operation state machine (OSM) model in MADL, and the other an optimized one based on the translated static-OSM model.
For each species, the 80 protein-coding gene sequences were translated to amino acids, were aligned using MAFFT aligner tool [ 43] and finally, the respective nucleotide sequences were aligned back based on the translated amino acids' alignment using back-translator tool from TreeBeST (http://treesoft.sourceforge.net/treebest.shtml).shtml
Since the original Los Alamos MSA does not always maintain the reading frame, codon-based MSAs were created for each gene based on the translated protein MSAs created using the MUSCLE program [ 40].
Phylogenetic analyses based on the translated sequences reiterate this relationship between R. flavefaciens and the Clostridia.
In the phylogenetic tree based on the translated AlkB amino acid sequences, all the Gordonia segregated clearly from other closely related genera.
In the phylogenetic tree based on the translated catA amino acid sequences, all the Gordonia segregated clearly from other closely related genera.
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Fragments of the A. carterae genes for psbB, petD and atpB were initially obtained by PCR using degenerate primers based on the corresponding translated gene sequences from A. operculatum and 'universal' primers to the core region (Table 1).
A 12th story, Taliesin, based on the bard and translated from a later manuscript, is included in some collections.
Another review assessed studies based on the DPP and translated into community settings such as churches [ 36].
The F. hepatica orthologous Dugesiidae sequences were determined with the blastx search based on the parasite's translated amino acid sequences (E value < 10−3).
The nucleotide sequences of each PCG were retroaligned based on the conservation of translated amino acids using DAMBE version 5.1.1 (Xia and Xie 2001).
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