next up previous contents
Next: About this document ... Up: QTL Cartographer Version 1.16 Previous: Bibliography   Contents


Index

additive effect
Rqtl
analysis
ANALYSIS
analysis phase
ANALYSIS PHASE
automatic actions
AUTOMATIC ACTIONS
background parameter
Zmapqtl Model Six
beta distribution
Rqtl
bootstrap
Log File | Bootstrapping | Permutations, Bootstraps and Jackknives | Eqtl
bootstraps, jackknives and permutations
BOOTSTRAPS, JACKKNIVES AND PERMUTATIONS
bug
Bug Reports
categorical trait
Other Traits | Simple Linear Regression
caveats
CAVEATS | CAVEATS | CAVEATS
command line
General Usage of the
composite interval mapping
Permutation Tests | Zmapqtl | JZmapqtl | Benchmarks
covariate
Permutation Tests | Eqtl
cross
advanced intercross
Experimental Design
backcross
Experimental Design | Output
Design III
Experimental Design
doubled haploid
Experimental Design
intercross
Experimental Design | Output
recombinant inbred line
Experimental Design | Experimental Design
repeated backcross
Experimental Design
test cross
Experimental Design
crosses
CROSSES
dominance
Rqtl | Dominant Markers
ECM algorithm
Computational Methodology
Eqtl
Permutation Test output | Eqtl | EQTL
options
Which Results?
output
Eqtl
experimentwise significance level
Permutation Test output
filename stem
Simulating/Reformatting Data | FILENAME STEM
ftp server
How to Get and | General tactics and notes | Using MAPMAKER/EXP
gamma distribution
Rqtl
gamma function
Rqtl
genetic linkage map
Definition of the Problem | Genetic Linkage Maps | Simulating a Map | Simulating Data
global behavior
GLOBAL BEHAVIOR
global command line options
GLOBAL COMMAND LINE OPTIONS
GNUPLOT
Gnuplot Copyright Information | Rmap | Output Flags | Printing Results | GNUPLOT
heritability
Rcross | Phenotypic Values | Phenotypic Values
hints
HINTS
inbred line
Experimental Design
information criteria
INFORMATION CRITERIA
input format
INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT | INPUT FORMAT
install
Macintosh
Macintosh
MS-Windows
MS-Windows
UNIX
UNIX
interactive menu
Automatic Mode | Interactive Mode | Prune
interval mapping
Permutation Tests | Zmapqtl | JZmapqtl | Benchmarks
jackknife
Permutations, Bootstraps and Jackknives | Eqtl
JZmapqtl
JZmapqtl | JZMAPQTL
option
JZmapqtl Options
least squares
Output
linear regression
Simple Linear Regression
LINPACK
LINPACK Copyright Information
LOD
Other Options | Preplot
log file
Log File
LR
Other Options | Preplot
LRmapqtl
LRmapqtl | LRMAPQTL
options
Simple Linear Regression
output
Output
Macintosh
Programming Philosophy | How to Get and | Working directory | Bootstrapping
binhex
Macintosh
install
Macintosh
StuffitExpander
Macintosh
mailing list
Mailing List
MAPMAKER
Genetic Linkage Maps | Filenaming Conventions | Using MAPMAKER/EXP files | Translating Data | MAPMAKER output files | MAPMAKER raw files
mapping function
Map Function
Fixed
Map Function
Haldane
Map Function
Kosambi
Map Function
maximum likelihood
Computational Methodology
MImapqtl
MImapqtl | MIMAPQTL
option
MImapqtl Options
missing data
Command Line Options
model
MODEL
models
MODELS | MODELS
MS-Windows
Programming Philosophy | Working directory | Bootstrapping
GNUPLOT
MS-Windows
Windows Explorer
MS-Windows
multiple interval mapping
MImapqtl
MULTIREGRESS
MULTIREGRESS
Note
Listing options | Verbosity | Resource File | Simulating/Reformatting Data | Rmap | Using MAPMAKER/EXP files | Input Files | Translating Data | Output
options
OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS | OPTIONS
output
OUTPUT
permutation test
Permutation Tests | Permutation Tests | Zmapqtl | Permutations, Bootstraps and Jackknives | Permutation Test output | Eqtl | Other Options
permutation tests
PERMUTATION TESTS
phenotype
Phenotypic Values
Preplot
PREPLOT
automagic
Preplot
options
Preplot
printing
Printing Results | Basic GNUPLOT
Prune
Prune | Permutations, Bootstraps and Jackknives | PRUNE
interactive menu
Pruning Datasets Interactively
Qstats
Qstats | QSTATS
options
Command Line Options
QTL
Definition of the Problem | Rqtl
QTLCART
QTLCART
Rcross
Rcross | RCROSS
input
Translating Data | Rcross input files
output
Output
references
REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES | REFERENCES
resource file
Resource File | General tactics and notes | RESOURCE FILE
Rmap
Rmap | RMAP
input
Rmap input files
input format
Rmap | QTL Cartographer user input
options
Simulating a Map | Command Line Options
output
Output Flags | Rmap output files
Rqtl
Rqtl | RQTL
input
Rqtl | Rqtl | Rqtl input files
output
Eqtl | Rqtl output files
sample
average deviation
Qstats
kurtosis
Qstats
mean
Qstats
skewness
Qstats
standard deviation
Qstats
variance
Qstats
simulation
cross
Simulating Data
gametes
Generation of Individuals
genetic linkage map
Simulating a Map
genetic model
Rqtl
missing data
Resampling data | Simulating Missing Data
QTL
Rqtl
random number seed
Random Number Seed
recombination
Generation of Individuals
trait
Phenotypic Values
SRmapqtl
Permutation Tests | Zmapqtl Model Six | SRMAPQTL
output
Output
standard deviation
Permutations, Bootstraps and Jackknives
stepwise regression
Permutation Tests | SRmapqtl
backward
SRmapqtl
forward
SRmapqtl
forward-backward
SRmapqtl
token
Rmap input files
UNIX
Programming Philosophy | How to Get and | General Usage of the
install
UNIX
using the individual programs
USING THE INDIVIDUAL PROGRAMS
variance
environmental
Simulating Data | Phenotypic Values
genetic
Phenotypic Values
verbosity
Verbosity
virtual marker
Eqtl
web site
Getting Help | General tactics and notes
window size
Zmapqtl Model Six
work code
WORK CODE
working directory
Working directory | Resource File | General tactics and notes | WORKING DIRECTORY
Zmapqtl
Permutation Tests | Zmapqtl | ZMAPQTL
model
Models
option
Zmapqtl Options
output
Output
virtual marker
Models



Christopher Basten 2002-03-27