Moreover, conserved regions with ICS are difficult to align well by one single alignment.
For each TFR we identified the single alignment net that contained the greatest number of alignable TFR bases, this ensured that each TFR could be mapped to no more than one loci in the second genome.
Therefore, whenever a single alignment error occurs, there is a chance that erroneously aligned views may attract more range data, creating clusters of correctly aligned views.
The deduced amino acid sequences of each of the 12 mt proteins of these species were aligned individually and then were concatenated into a single alignment.
For each reference alignment, a "combined score" was calculated corresponding to the maximal score possible if all correctly aligned blocks from each program were combined in a single alignment.
After cleaning up the nucleotide alignments for poorly aligned regions, the 1,486 multiple alignments were concatenated in a single alignment of 431,655 codons.
The corresponding nucleotide sequences were retro-aligned, using the PAL2NAL webserver [ 25], and then concatenated into a single alignment.
By decreasing the gap penalty between the two haplotypes, we created a single alignment of the reference region around gene GB45615 that included the reads formerly aligned to GB49510 to analyze the insertions and deletions.
As the pits in a single alignment on both sides of the indentation show equivalent asymmetry, they must represent the surface intersection of asymmetrically shaped dislocation loops.
Each fragment was simulated independently and then concatenated into a single alignment.
The 1,197 protein sequence alignments were concatenated into a single alignment for phylogenetic inference.
