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To generate an initial ML estimate for final optimization and support estimation, we performed 11 ML searches from 11 parsimony starting trees generated under the default parsimony model in RAxMLv7.2.8.
Marker data then were uploaded to Design Studio v1.5 and probes were generated under the default conditions, with the hg19 human genome assembly (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/) used for probe reference.
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By default, a random pyholgenetic tree is generated under the Yule-Harding model [31], [32], but alternatively, user-defined trees can also be loaded.
Selected output from the application is provided here as an example of the type of results generated under default settings.
Ct values were generated using the default analysis settings.
Box plots were generated using the default R software options.
Homology models were generated using the default settings with the Amber99 forcefield and medium model refinement.
The alignments were generated using the default settings (http://gel.ahabs.wisc.edu/mauve/, last accessed August 29 , 2014.
Then, the functional linkage could be generated using the default setting.
A starting chronogram that replaced the UPGMA default tree and satisfied all UCLN priors was generated under PL in r8s.
Models were generated using the model-default script from the MODELLER package v9.12 (http://salilab.org/modeller/).
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