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A multi-sequence alignment was created in MEGA 5.2 [ 65] with the implemented MUSCLE algorithm [ 66].
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The orthologous protein sequences were aligned using the method implemented in muscle [ 31].
Currently, the most promising approaches are those implemented in Muscle and Mafft.
The alignment method of the other two phylogenetic analyses was implemented on MUSCLE 3.6 [ 75] and the conserved region of each alignment was trimmed using Gblocks [ 76], which allows less strict flanking positions and gap positions within the final blocks, but does not allow many contiguous nonconserved positions.
The DNA sequences were aligned using the program MUSCLE implemented in the software MEGA5 (Tamura et al. 2011) with minor manual adjustments.
In order to maximize the potential therapeutic effects of cells and growth factors, several biomaterial based strategies have been developed and successfully implemented in animal muscle injury models.
and then sequenced using an ABI PRISM dye terminator cycle sequencer, model 3700 (Applied Biosystems, Foster City, California, U.S.A .. DNA sequences were aligned using the program MUSCLE implemented in the software MEGA5 (Tamura et al.2011) with subsequent manual adjustments.
Other parts of the model (F V relationship and passive elements) are not dependent on the initial CE length and, therefore, they are implemented for the muscle as a whole rather than for the individual motor-units.
These predicted CDS were globally aligned to each other using muscle (implemented through Geneious).
Codons of insect sequences of usp and cox1 genes were aligned using the program Muscle implemented in SeaView [ 64].
The Muscle (implemented in the software MEGA) [ 66], ClustalW2 [ 67], and Guidance methods [ 68] were all tested to obtain a reliable multiple sequence alignment.
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