Contents

• Quick Start
  • Loading data
  • Linkage groups and 2-Points estimations
  • Building maps from scratch
  • Map improving methods
  • Order validating methods
  • Building framework maps
  • Merging data sets
  • Dealing with ``double markers''
  
  
• User and reference documentation
  • Formatting the data
    • Genetic data sets
    • Radiated Hybrid data sets
    • Constraints data sets
    • Reference order data sets
  • Loading and Merging data sets
    • dsload
    • dsmergen
    • dsmergor
    • heapequiset
    • dsinfo
    • dsget
  • Markers, linkage groups and 2-points estimations
    • mrkallget
    • mrkdist2p
    • mrkfr2p
    • mrkid
    • mrkinfo
    • mrklast
    • mrklod2p
    • mrkdouble
    • mrkmerge
    • mrkmerges
    • mrkmerget
    • mrkname
    • mrkselget
    • mrkselset
    • mrkadd
    • mrksub
    • mrkdel
    • group
    • groupget
    • groupmerge
    • multigroup
  • Maps and the Heap
    • The heap
    • heapsize
    • heapsizeget
    • heaprint
    • heaprintd
    • heapget
    • heapordget
    • maprint
    • maprintd
    • maprintdr
    • bestprint
    • bestprintd
    • mapget
    • mapordget
    • mapocb
    • heaprinto
  • Building maps from scratch
    • Comprehensive mapping
    • sem
    • cgtolerance
    • nicemapl
    • nicemapd
    • mfmapl
    • mfmapd
    • lkh
    • lkhn
    • lkhl
    • lkhd
    • lkhocb
    • lkhocbn
    • cg2tsp
    • fconcorde
    • build
    • Framework mapping
    • buildfw
    • cgrobustness
    • cgnotrobust
    • frameworkmst
    • framework
  • Improving and validating existing maps
    • Simulated annealing
    • Taboo search
    • Genetic algorithm
    • flips
    • polish
    • squeeze
    • annealing
    • greedy
    • algogen
    • mcmc
    • Interrupting
  • Comparative mapping
    • Replacing the traditional criterion by the comparative mapping criterion
    • dsbplambda
    • Building a Pareto frontier from scratch
    • paretolkh
    • paretolkhn
    • paretoheapsize
    • Improving an existing Pareto frontier
    • paretogreedy
    • paretogreedyr
    • Finding the best map in an existing Pareto frontier
    • paretobestprint
    • paretobestprintd
    • paretoplotg
    • paretosave
    • Computing the number of breakpoints
    • mapbp
    • dsbp
  • System commands
    • cgout
    • cgversion
    • cglicense
    • cgstat
    • cgrestart
    • quietset
    • verbset
    • cgsave
    • cgexport
    • cg2pt
  
  
• Bibliography
• Index