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Acknowledgements
Contents
Index
Carthagène - User Documentation
T. Schiex, T. Faraut, S. de Givry, D. Leroux, B. Servin
INRA
C. Nelson
Acknowledgements
Contents
Introduction
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
Backcross data
Intercross F2 data
Recombinant inbred lines (RIL) data
Data from arbitrary series of mating operations in line crosses
Phase known outbred data
Radiated Hybrid data sets
Constraints data sets
Reference order data sets
Loading, Correcting and Merging data sets
dsload
dsmergen
dsmergor
heapequiset
dsinfo
dsget
dsrhconv
imputation
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
cgprecision
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
Thomas Schiex 2018-03-23
