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When the rotational sampling is performed at 45° intervals, the performance is marginally improved to 2.7° (Table 1), indicating that the 60° interval is already sufficient for most alignment refinements.
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HP carried out gene structure prediction, phylogenetic analysis, alignment refinements, and protein analysis.
Aligned sequences were exported from ARB into Mesquite for manual alignment refinement.
An iterative alignment refinement strategy as described in Tóth et al.48 was employed: maximum-likelihood gene trees computed from preliminary alignments (using RAxML, see below) were used as guide trees for the next round of multiple alignment for PRANK.
A computer-based program, Gblocks, was used for alignment refinement.
Alignment refinement was done with Gblocks software (version 0.91b) [ 99].
To perform a complete alignment refinement this process must be repeated iteratively until convergence is achieved (next section).
KM conducted all molecular data analyses except alignment refinement (done by CM) and rogue taxon analyses (done by AJA).
Most alignments ranged from 70 82 amino acids.
These are drawings of the most arcane refinement, unearthly beautiful.
Perhaps the most engaging alignments occur in impressive layouts of hand-painted lead soldiers.
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