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In this alignment, the order of 11 of these in silico maps agreed with the order suggested by the genetic map (after reorienting three in silico maps).
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The assessment capability claimed by Samadani et al. appears to be variability of binocular alignment on the order of 0.01° magnitude.
To quantify the number and size of recombination tracts, we concatenated the multiple alignments following the order of the A. baumannii ATCC 17978 strain and fetched 688 recombination events significantly highlighted by three procedures (RDP3, CHI2, and GENECONV, see Materials and Methods).
It is apparent that the final multiple gene order alignment is sensitive to the order of alignment steps.
(Note that some of the structural alignment algorithms ignore the order of the atoms on the backbone, but we do not change the order of the atoms in this paper).
Secondly, the pairwise alignments take in the order of 1 CPU year per genome we aligned against the pig genome.
Runtimes also suggest that Hapler will be useful in practice for whole-transcriptome assemblies, where contig alignments are on the order of a few kilobases in length.
In contrast, when the level of heterotachy is weak (e.g. τ = 0.2) and the alignment size is in the order of magnitude of the currently used ones (5,000 amino acids), the homotachous (one component) model is preferred.
Note that forward transitions are genomic transitions between a pair of aligned positions that lie on the same sequence (i.e. G, G′, S or S′) such that the order of alignment is preserved with respect to the alignment direction (e.g. when aligned to complementary strand order will be reverse as well).
Stripped alignments were concatenated in the order of orthologous group numbers as assigned by OrthoMCL.
Two alternative Syntenator multiple gene order alignments of mouse (M), rat (R), human (H) and dog (D) are shown to demonstrate the dependence of the alignment outcome on the alignment order of species.
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