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The optimal overall marker order was inferred following the protocol described by Niehuis et al. [33].
The expected marker order was confirmed using the "flips" option of Cri-Map v2.
The marker order was finalized using RECORD [ 55].
Local marker order was determined by multipoint analysis.
When a better marker order was established after FLIPS5, marker order was resolved and FLIPS5 was re-run until no further changes were apparent.
The marker order was refined using RECORD [ 40] and the goodness-of-fit of the marker order was examined by plotting pairwise recombination fractions against LOD linkage statistics.
Once the markers were assigned to linkage groups relative marker order was determined as described below.
The marker order was generally well conserved between the individual and consensus maps.
The most likely marker order was determined as the common order shared by most of maps.
The final integrated marker order was projected onto a common relative scale representing all markers.
Initial marker order was calculated with orderMarkers, using the Kosambi map function.
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