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The JMMAP program estimated the maximum likelihood map using the Kosambi distances.
Linkage group assignment and ordering of loci was established based on TMAP software [ 50] that finds the maximum likelihood map using an error-compensating model.
The table in Additional file 1 lists the reassembled marker contigs, their inferred hox gene class, and maximum likelihood map positions.
EBI 847 maps to Miscanthus linkage group Ms16 at 36.8 cM on the integrated map (41.2 cM on the GF maximum likelihood map) while EBI 848 is placed on linkage group Ms17 at 19.2 cM on the integrated map (20.1 cM on the UN maximum likelihood map).
The JoinMap JMREC was used to estimate pairwise cM distances between all pairs of informative loci in each linkage group and JMMAP to find the maximum likelihood map using the Kosambi distances.
To validate the map ordering of CRI-MAP, markers belonging to a large linkage group with a range of informative loci (LG8 - established by AUTOGROUP in CRI-MAP) were chosen to build an independent sex-average comprehensive linkage map with CarthaGène version 1.0 which incorporates an EM (expectation-maximization) algorithm and a local search technique to build a maximum likelihood map [ 26].
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Marker ordering calculation was done with the maximum likelihood mapping algorithm.
These linkage groups were ordered using JoinMap's maximum likelihood mapping algorithm.
Maximum likelihood mapping is a useful tool for analyzing and depicting the mosaic nature of genomes.
Genetic maps were estimated for each population using the Maximum Likelihood mapping algorithm for CP populations implemented by JoinMap (v4.1).
The maximum likelihood mapping (MLM) algorithm (using default parameters) was used to order the markers in the respective groups.
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maximum sensitivity map
maximum likelihood modeling
maximum scoring map
maximum likelihood estimation/estimator
maximum likelihood reconstruction
maximum likelihood learning
maximum likelihood dendrogram
maximum likelihood ratio
maximum amplitude map
maximum likelihood tree
maximum likelihood estimation
maximum likelihood approach
maximum likelihood extraction
maximum likelihood estimator
maximum runout map
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