... file^1.1

This file has been extracted from the MapMaker 3 distribution.

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... distances^1.2

When used on two data sets of the same type, this merging process corresponds to the addition of information on new individuals (on new or known markers). It must not be used when new markers are types on existing individuals. In this case, the data-set file must directly be edited by adding new lines for the new markers (and changing the number of markers in the header).

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... heap''^2.1

This is the usual name for the data structure [CLR90] used in CARTHAGENE to actually store the map. In practice, a hash map is also used to check if a map aready appears in the heap.

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... ordering^2.2

Which is closely related to the so-called travelling salesman problem, an NP-hard problem.

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... flipped ^2.3

This is called a 2-OPT move

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... frontier^2.4

This term comes from the field of Multiobjective Combinatorial Optimization.

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... markers^2.5

The maximum number of maps in the Pareto frontier is equal to the number of selected markers minus one.

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... markers^2.6

a marker with no known orthology information is approximated by temporally adding the marker in the reference order such that the marker is the singleton element of a dummy chromosome.

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...dsmergor)^2.7

The 2-point loglikelihood contribution between two adjacent markers occurring in two different datasets is equal to zero.

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... likelihood^2.8

Except in the case of the fast EM mode set by the cg2pt command.

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... one^2.9

An obligate breakpoint occurs between two adjacent markers from two different chromosomes in the reference genome.

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