Genes common to all three C. raciborskii strains were each aligned as orthologous clusters using Muscle [ 47] and the alignments assessed for synonymous, non-synonymous and indel mutations.
Global alignments assess end-to-end sequences and local pairwise alignments search for regions with high identity.
Users can edit these alignments, assess phylogenetic utility among detected loci, infer preliminary phylogenies (if appropriate), or proceed with downstream development of individual loci for phylogenetic applications (Figs. 2 and 3).
In each case, a guide tree was constructed using Clustal and the quality of the alignment was assessed by comparing the alignment of the included HOMSTRAD sequences against the HOMSTRAD reference alignment.
Each individual alignment was assessed for congruence with respect to a combined matrix including unambiguously aligned regions of every gene.
The quality of the alignment was assessed by blending or flickering between the adjacent images.
After applying the ring, external fixator alignment was assessed and corrected.
After applying the ring fixator alignment was assessed and corrected if needed.
When the initial correction program was completed, the limb alignment was assessed by long leg standing AP radiographs (Fig. 3).
