#define HELP_GENERAL 1
/* general
Help is available for several commands in GMendel using the 'help'
command. Use 'help commands" to see a list of many of the commands in
GMendel. Use 'help print' to see a list of the output commands
available in GMendel. Use 'help set' to see a list of the parameters
that may be adjusted.
*/
#define HELP_COMMANDS 2
/* commands
load		Load a data file
compute		Compute statistics, linkage groups, loci order, ...
print		Show results of computations in many formats
set		Set a parameter to a particular value
help		Print help on a specified topic
quit		Exit GMendel
reverse		Invert the order of a linkage group
include		Include a locus in a particular group
exclude		Remove a locus from a particular group
join		Merge two linkage groups
*/
#define HELP_PRINT 3
/* print general
There are a number commands used to print information that has been
computed by GMendel. When GMendel is started, the results of the print
commands are sent to the screen. These results can be sent to a file
by using the 'set output' command to open a file that will take all
output until further notice. See 'help output' for details.

print datafile		Show data GMendel has read
print single		Sinlge locus statistics
print percent		Percent of the r values estimated
print g			G stat for linkage for all pairs of loci
print r			Recombination frequency for all pairs of loci
print group		Show the linkage groups
print order		Show the order of loci within linkage groups
print interorder 	More detailed information on order of loci
print rgroup		Recombination frequency for pairs within group
print ggroup		G stats for all pais within a group
print gordered		G stats for adjacent ordered locus pairs
print gpordered		Include significance level with 'gordered'
print lodgroup		Show LOD scores for all pairs within a group
print crossovers	Ordered phenotype data to highlight crossovers
print psmap		Print a postscript map of a group into a file
print newpage		Put a page break on the screen or file
print distribution	Show the observed phenotypes between two loci
view group		Display a postscript map on the screen
make ascii profile	Tool to investigate improper grouping
make profile		Creates a file to be viewed using gnuplot
view profile		On screen tool to search for improper grouping
print options		Display the options and parameters
close			Close a postscript or output file
*/
#define HELP_SET 4
/* set
The set command is used to define a value of some variable in the
GMendel program. To use the set command, type 'set <param>' or 'set
<param> <value>' where <param> is one of the following values. Help is
available for each of the following parameters. See the help for
simulated annealing for the associated parameters.

width		display screen width
height		display screen height
minlod		minimum significan LOD score for grouping loci
gsark		k used in the gsar function -- 'help gsar' for details
rmax		maximum recombination frequency for grouping loci
cutoff		Maximum group size to use exhaustive search on
function	Selects a function to evaluate a group ordering
fold		option to replace a large r (>.5) with 1-r
kmap		parameter used in the map distance function
optimize	select between simulated annealing and hybrid
output		specify a file to record the output of GMendel
psfile		open a postsript file for a linkage map
psfont		specify a font size for the postscript map
psbarheight	specify the height of the postscript map
psskip		minimum vertical spacing between loci on map
psadd		print sum of distances on postscript maps
subgroup	select a subset of the datafile (complex mating types)
segregation	correct for segregation distortion
significance	set the significance level for a number of statistics
*/
#define HELP_RMAX 5
/* rmax
Given the values rmax and minlod, equivalence classes of the loci are
computed. A locus belongs in a particular equivalence class if the r
value between that locus and some locus in the equivalence class is
less than rmax and the LOD score between the two loci is greater than
minlod. The maximum allowable recombination frequency, or rmax, is
typically set to 0.3 or smaller. This causes loci that tend to remain
together after recombination events to be members of the same group.
The value of RMAX is set with the 'set rmax' command.
*/
#define HELP_PMAX 6
/* pmax
The 'set pmax' command is old and no longer has any effect in GMendel.
*/
#define HELP_OUTPUT_FILE 7
/* output
The results from GMendel can be saved to a file using the 'set output'
command to redirect the output from the screen to a file. The set
output command will ask for a filename (or 'set output <filename>')
and all subsequent output, including the GMendel prompt, will be put
in the specified file, not to the screen. To return the output to the
screen, give the command 'set output stdout'. If later, the output
should again be redirected to the file, give another 'set output'
command and all output from gmendel will be appended to the specified
file.
*/
#define HELP_DEBUG 8
/* debug
The debug parameter is generally not useful to the user of GMendel,
but may be of use to people modifying GMendel. The value of debug is
set between 0 and 100, the higher the value, the more debugging
information printed. This option will not be available unless GMendel
has been compiled with the -DDEBUG flag set (See the gmendel.h file).
*/
#define HELP_OPTIMIZE_METHOD 9
/* saoptimize
Two optimization methods are available to order the loci of a group,
exhaustive search and simulated annealing. Since the exhaustive search
method takes a vary long time as the number of loci in a group grows
above about 8, it can not be used alone, but is used in combination
with the simulated annealing method. In Gmendel, the optimization
function can be purely simulated annealing, or it can be exhaustive
search for small groups of loci and simulated annealing for larger
groups of loci. To choose simulated annealing, use the command 'set
saoptimize sa'. To choose the combination of exhaustive search and
simulated annealing, use the command 'set saoptimize hybrid'. The size
of the largest group that an exhaustive search will be used for in the
hybrid optimization method is set by the cutoff parameter, see 'help
cutoff'.
*/
#define HELP_OPTIMIZE_CUTOFF 10
/* cutoff
Using the combination of exhaustive search and simulated annealing to
order groups of loci requires some point to switch from using the
exhaustive search method to the simulated annealing method. The value
of the cutoff parameter is the largest group of loci that the
exhaustive search method will be used on. Since the number of
orderings of the loci in a group grows as the factorial of the number
of loci in the group, it is not recomended that cutoff be set larger
than 8. The command 'set cutoff 7' will cause GMendel to used
exhaustive search for all groups with 7 or fewer loci when using the
hybrid optimization method.
*/
#define HELP_SEGRAGATION_DISTORTION 11
/* segregation
GMendel will correct the expected genotype distribution based on the
gamete distribution in the data. By setting the segragation parameter
to true, GMendel will correct for segragation distortion.  When the
segragation parameter is set to false, no correction will be made.
The command 'set segragation true' and 'set segragation false' are
used to turn on or off the segragation distortion correction. If the
command 'set segragation' is given with no value, the value of the
segragation parameter is switched.
*/
#define HELP_K_FOR_MAP_FUNCTION 12
/* kmap
In 1979, Felsenstein gave a mapping function that generalized both the
Haldane and the Kosambi mapping functions. By setting the parameter
kmap to 1.0, the mapping funciton will be equivalent to the Haldane
mapping function. By setting the parameter kmap to 0.0, the mapping
function will be equivalent to the Kosambi mapping function. The
values 0.0 <= kmap < 2.0 are the legal values for Felsenstein's
mapping function.
*/
#define HELP_SA_INITIAL_TEMPERATURE 13
/* sainitial
The temperature in the simulated annealing algorithm is roughly
analogous to how vigorously the order of the loci in the group are
rearranged between the original ordering and the new ordering. The
higher the temperature, the more the original ordering is mixed up to
get the new ordering. The advantage of a high temperature is that many
well seperated orderings will be tested, but very few of the total
number of orderings will be tested. The advantage of a low temperature
is that many of the orderings that are 'close' to the original
ordering will be tested, but very few of the 'distant' orderings are
tested.  The default value of the initial temperature is set to five.
It may be possible to choose a better inital value that will produce
more accurate results using less computer time. The command 'set
sainitial <n>' will set the initial temperature to <n>. (See also
sadecrease)
*/
#define HELP_SA_TEMP_DECREASE 14
/* sadecrease
The simulated annealing algorithm attempts to find the rough ordering
by using a high temperature and then gradually refines this ordering
by lowering the temperature. (See sainitial) The rate the temperature
is decreased is controlled by the sadecrease parameter. During each
iteration of the outer loop of the simulated annealing method, the
temperature is multiplied by the sadecrease parameter. Setting this
parameter to a value just slightly less than 1.0 (0.9975) will result
in the program running for a long time, but producing more accurate
results.  Setting the the parameter to a value significantly less than
1.0 (0.75) will result in the program running very quickly, but
producing less accurate results.  The value of this parameter is set
with the 'set sadecrease' command. If the value is not set by the
user, a value is computed by the GMendel program depending on several
other parameters. Changing this value should be done cautiously.
*/
#define HELP_SA_PROPORTION 15
/* saproportion
As the temperature in the simulated annealing algorithm decreases, the
number of position in the loci ordering that are changed is decreased.
To compute the number of positions in the ordering to change, the
temperature is multiplied by the number of loci in the group and this
is then multiplied by the parameter saproportion. It is initially set
to 0.25.  If it is felt that the loci ordering is not being 'mixed up'
enough, saproportion should be increased.  If it is felt that the loci
ordering is being 'mixed up' too much, saproportion should be
decreased. This parameter is not sensative so doubling or halving
saproportion is fine.
*/
#define HELP_SA_K2 16
/* sak2
The simulated annealing method will occasionally accept an ordering of
the loci that is actually worse than the original ordering. This gives
the method an opportunity to escape from local minima. The probaility
of accepting an ordering that is worse than the original ordering is
directly proportional to the difference in the scores of the new
ordering and the current ordering.  The probability of accepting is
inversly proportional to the product of the temperature and a
constant, k2. Increaseing the value of k2 decreases the probability of
accepting an ordering that is worse than the current ordering.
Decreasing the value of k2 increases the probability.
*/
#define HELP_SA_NO_CHANGE_INNER_LIMIT 17
/* sainnerchange
The simulated annealing method has two major loops, an inner loop and
an outer loop. During each iteration of the outer loop, the
temperature is decreased and the inner loop is run many times. The
inner loop normally terminates after the ordering has been changed a
number of times without improving the score of the ordering. The inner
loop is terminated after the number of iterations of the inner loop
without improving the score is greater than the sainnerchange
parameter.
*/
#define HELP_SA_NO_CHANGE_OUTER_LIMIT 18
/* saouterchange
The simulated annealing method has two major loops, an inner loop and
an outer loop. During each iteration of the outer loop, the
temperature is decreased and the inner loop is run many times.  The
inner loop normally terminates after the ordering has been changed a
number of times without improving the score of the ordering. The outer
loop is terminated after the number of iterations of the inner loop
without improving the score is greater than the saouterchange
parameter.
*/
#define HELP_SA_MAX_INNER_LIMIT 19
/* sainnerlimit
The simulated annealing method has two major loops, an inner loop and
an outer loop. During each iteration of the outer loop, the
temperature is decreased and the inner loop is run many times. The
maximum times that the inner loop is run is set by the sainnerlimit
parameter. This acts as a 'secondary' cutoff for the inner loop and
should be set high. If things are working properly, the inner loop
should be terminated by the sainnerchange parameter.
*/
#define HELP_SA_MAX_OUTER_LIMIT 20
/* saouterlimit
The simulated annealing method has two major loops, an inner loop and
an outer loop. During each iteration of the outer loop, the
temperature is decreased and the inner loop is run many times. The
maximum times that the outer loop is run is set by the saouterlimit
parameter. This acts as a 'secondary' cutoff for the outer loop and
should be set high. If things are working properly, the outer loop
should be terminated by the saouterchange parameter.
*/
#define HELP_PRINT_PS_FILE 21
/* psfilename
GMendel will generate a map of each group with more than one loci.
These maps can then be printed on a postscript printer. To indicate
that the maps should be created, the parameter psfilename is set to
the name of the file to receive the maps. The command 'set psfilename'
is given and GMendel will ask for a filename (or 'set psfilename
<name>) and then GMendel will try to open the file for writing. The
user of GMendel must give a filename (or pathname) that can be written
to.
*/
#define HELP_PRINT_PS_MAP 22
/* print psmap
The command 'print psmap' assumes that a file has been opened using
the 'set psfilename' command for the postscript map. The 'print psmap'
command computes the maps for all linkage groups and saves them in the
file specified by the 'set psfilename' command. Maps of individual
groups may sent to the psmapfile by using the command 'print psmap 2'
to print a map for group 2. Maps for several groups can be sent using
the command 'print psmap 2 3 5'.

The left side of the map lists the members of the linkage group in the
order computed by GMendel. The numbers on the right side of the map
are the recombination percentages between adjacent loci. The
horizontal lines crossing the vertical bar represent the relative
positions of the loci within the group. If the parameter psadd is true
('set psadd'), the numbers on the right side of the map will be the
sum of the distance from the bottom locus on the map.
*/
#define HELP_PS_FONT_SIZE 23
/* psfont
The size of the font used in the postscript maps is set using the 'set
psfontsize' command. It is initially set to 10, for ten point fonts. This
value should be an integer.
*/
#define HELP_PS_BAR_HEIGHT 24
/* psbar
The height of the bar that represents the map in the postscript maps
is set using the 'set psbarheight' command. The value of psbarheight
is a real number and is the bar height in inches. It is initially set
to 9.0.
*/
#define HELP_PS_SKIP 25
/* psskip
The spaceing between adjacent loci names and the statistics printed on
the postscript map is controlled using the 'set psskip' command. The
initial value is 1.0 and indicates single spacing, a value of 1.5
indicates one and a half spacing. The value should be a real number.
*/
#define HELP_HELP 26
/* help
The help command is usually followed by the name of a topic that help
is requested for. For example 'help set' will produce a list of the
parameters that can be set and 'help include' will give instructions
on using the include command. To quit the help system, type 'quit' at
the help prompt.
*/
#define HELP_QUIT 27
/* quit
The quit command will terminate the execution of the GMendel program.
There are several synonyms that will also terminate the execution of
GMendel. Unlike most of the other command in GMendel, quit and its
synonyms must be completely typed out.
*/
#define HELP_WARRANTY 28
/* warranty
NO WARRANTY

11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
OTHER PARTIES PROVIDE THE PROGRAM ``AS IS'' WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
PROGRAM IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
*/
#define HELP_COPYRIGHT 29
/* copyright
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or (at
your option) any later version.  This program is distributed in the
hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  See the GNU General Public License for more details.  You
should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation,
Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
#define HELP_COMPUTE 30
/* compute general
There are three quantities that GMendel will compute; stats, groups,
and orders. Stats are the single locus and pairwise statistics, groups
are the locus grouping, and order is the order of the loci within each
linkage group.  The stats must be computed before the groups, and the
groups must be computed before the orders. If the orders are requested
and the stats and groups have not been previously computed, GMendel
will first compute the stats and groups before computing the order.
By breaking the computations up into seperate pieces, it is possible
to change various parameters and recompute the ordering without having
to recompute the stats or groups. Changing certain parameters will
require some recomputation, for instance, changing either rmax or
minlod will require that the groups be recomputed. When groups are
recomputed the ordering of those groups must be recomputed.

Further information is available for 'compute stats', 'compute
groups', and 'compute orders' by giving the command 'help compute
stats' and so on.
*/
#define HELP_COMPUTE_STATS 31
/* compute stats
The 'compute stats' command computes a number of statistics that
usually only need to be computed once in GMendel. Once these
statisitics are computed different groupings and orders can be
computed without wasting CPU time recomputing these statistics.  The
statistics are divided into two catagories, single locus statistics
and two locus statistics.

The single locus statistics are a G statistic for genotypic
distribution, the significance of this G statistic, a G statistic for
gametic distribution, and the significance of this G statistic. When
there is more than one population in the data file, a seperate set of
statistics is computed for each population and a pooled set of
statistics is computed for the combination of all of the populations.

The two locus statistics are G statistics for pairs of loci and
recombination frequencies for pairs of loci. Again, when there is more
than one population in the data file, seperate statistics are computed
for each population and a pooled set of statistics is computed for the
combination of all populations.
*/
#define HELP_COMPUTE_GROUPS 32
/* compute groups
The 'compute groups' command divides the loci into linkage groups. A
maximum acceptable r value (rmax) and a minimum acceptable LOD score
(minlod) are specified using the 'set rmax' and 'set minlod' commands.
Given the values rmax and minlod, equivalence classes are computed. A
locus belongs in a particular equivalence class if the r value between
that locus and some locus in the equivalence class is less than rmax
and the LOD score between the two loci is at least as large as minlod.

The maximum allowable recombination frequency, or rmax, is typically
set to 0.3 or smaller. This causes loci that tend to remain together
after recombination events to be members of the same linkage group.
The minimum LOD is usually set to 3.0 or larger.

The compute groups command requires that the 'compute stats' command
have been run previously. If the compute stats command has not been
given, it will be run and then the compute groups command will be run.
The results of the compute groups command can be viewed with the
'print groups' command.
*/
#define HELP_COMPUTE_ORDERS 33
/* compute orders
The compute orders command takes the information computed from the
compute stats and compute groups commands and computes an ordering for
the loci in a group or groups. The order for larger groups is computed
using the simulated annealing method. This method allows GMendel to
compute an approximate ordering relatively quickly. For smaller
groups, an exhaustive search can be used to find the ordering that
minimizes the objective function.

There are a number of parameters that can be set to guide the
computation of the loci orders. The parameters cutoff, function,
optimization function, sadecrease, sainitial, sainnercutoff,
saoutercutoff, sainnerlimit, saouterlimit, sak2, and saproportion are
all used to control the operation of the simulated annealing method.
Of particular importance are the parameters function, sainnercutoff,
and saoutercutoff. The command help followed by any of these parameter
names will give more information about the parameter.

Orders can be computed for a single group by giving the command
'compute order 3' or a list of groups by using the command 'compute
order 3 5 6'. The command 'compute order' will compute orders for all
groups.
*/
#define HELP_NEWPAGE 34
/* print newpage
The 'newpage' command will print a character in the output that should
cause the printer to page feed. Any subsequent output should start at
the top of the next page.
*/
#define HELP_PRINT_OPTIONS 35
/* print options
There are several parameters that can be modified in GMendel. The
'print options' command will print a list of the values of the various
options and parameters.
*/
#define HELP_PRINT_ORDER 36
/* print orders
The 'print orders' command will print the locus order of each group
along with the r values between each adjacent pair of loci and the sum
of the r values. The total number of order evaluations is given for
each group.  Orders can be printed for a single group by giving the
command 'print orders 3' or a list of groups by using the command
'print orders 3 5'.  The command 'print orders' will print the orders
for all groups.
*/
#define HELP_PRINT_DATA_FILE 37
/* print data
After GMendel has read a data file, the command 'print data' will
print a copy of the data file. The contents of this report is the same
as is in the data file, but the format should be a little easier to
read. It may be useful to proof read the data in the data file.
*/
#define HELP_PRINT_SINGLE_LOCUS_STATS 38
/* print single
The command 'print single' presents the G statistic and its
significance for the distribution of the genotypes in each locus and
the G statistic and the significance for the gamete distribution in
each locus. The format of the report depends on the number of
populations in the data file. For a single population, one line
containing the four statistics is printed for each loci.  When there
is more than one population in the data file, four lines are printed
for each loci. The first line reports the G statistic for the genotype
distribution in each of the populations and a pooled G statistic for
the genotype distribution over all of the populations.  The second,
third, and fourth lines are similar for the three other statistics.
Each report also give the distribution of phenotypes in the
population.
*/
#define HELP_PRINT_GROUP 39
/* print groups
A list of the linkage groups is printed by the 'print groups' command.
Each locus is represented by the short name it is given in the data
file. Each group is preceded by the text 'group #<x>:' where <x> is an
integer. This number is what is used to refer to that group. The
command 'print groups 3 5' will print only the two groups labeled with
3 and 5. There are several other commands where the groups can be
specified using these group numbers.
*/
#define HELP_PRINT_G_STATS 40
/* print gstats
The 'print gstats' command will print the G statistic between all
pairs of loci. If there is exactly one population in the data file, a
simple table of the G statistic and its significance between each pair
of loci is printed. If there is more than one population, a seperate
line is printed for each pair of loci, the first column is the G
statistic and its significance for the first population, the second
column for the second population and so on. The last column is the
pooled G statistic and its significance over all populations for the
pair of loci.
*/
#define HELP_PRINT_PAIRWISE_R 41
/* print rgroup
The 'print rgroup' command will print the recombination frequency
between all pairs of loci in a particular group. Without specifying
any groups the command will print a table of recombination frequency
values for each group. Tables can be printed for specific groups, for
example 2 and 5, using the command 'print rgroup 2 5'. If there is
more than one population, the pooled r values for each pair of loci
are printed.
*/
#define HELP_PRINT_COMPLETE_PAIRWISE_R 42
/* print rcomplete
The 'print rcomplete' command will print the recombination frequency
between all pairs of loci. If there is exactly one population in the
data file, a simple table of recombination frequency, variance, and
LOD scores, between each pair of loci is printed. If there is more
than one population, a seperate line is printed for each pair of loci,
the first column is the recombination frequency, variance, and LOD
score for the first population, the second column for the second
population and so on. The last column is the pooled recombination
frequency and variance over all populations for the pair of loci.
*/
#define HELP_CLOSE 43
/* close
The output file and the postscript map file may be closed before the 
GMendel program is exited using the 'close outfile' and the 'close psmap'
commands. Closeing a file allows that file to be examined or printed.
*/
#define HELP_RECOMPUTE_TEMP 44
/* reset temp
The default value for the temperature decrease factor (a simulated
annealing parameter) is actually a function of the initial temperature
and the maximum number of iterations in the outer loop without an
improvement in the score. When either of the these parameters are
changed, the temperature decrease factor needs to be recomputed using
the 'reset temp' command. See 'help sadecrease' for details of the
temperature decrease parameter.
*/
#define HELP_INCLUDE 45
/* include
The inlcude <locus_name> <group_number> command lets the user place
the specified locus in the selected group. The locus_name should match
the name given to one of the loci in the data file. The case of the
letters in the name is important. The group_number should be an
integer representing one of the groups that already exists. See also
the exclude command.
*/
#define HELP_EXCLUDE 46
/* exclude
The exclude <locus_name> <group_number> command lets the user remove
the specified locus from the selected group.  The locus_name should
match the name given to one of the loci in the data file. The case of
the letters in the name is important. The group_number should be an
integer representing one of the groups that already exists. See also
the include command.
*/
#define HELP_GSAR_K 47
/* gsark
The generalized SAR function evaluates an ordering of the loci by
taking the sum of the recombination frequency of loci that are
adjacent, loci that are seperated by one loci, loci that are seperated
by two loci and so on.  The gsar_k parameter is the largest seperation
between loci that will be considered when computing the value of the
generalized SAR function. It is set with the 'set gsark <n>' where
<n> is an integer.
*/
#define HELP_LOD 48
/* minlod
The LOD score is a test statistic which can be used to test the null
hypothesis of no linkage against the alternate hypothesis of linkage.
The type I error probability of a LOD score Z is 10 to the -Z power.
The min_lod parameter is used to find linkage groups. Any two loci
with a LOD score greater than min_lod will be put in the same linkage
group.  The default value for min_lod is 3.0 and can be changed with
the 'set minlod' command.
*/
#define HELP_PRINT_LOD 49
/* print lod
The LOD score is a test statistic which can be used to test the null
hypothesis of no linkage against the alternate hypothesis of linkage.
The type I error probability of a LOD score Z is 10 to the -Z power.
Printing the pairwise LOD scores for a group can be used to help
determine if there is more than one physical linkage group in the
linkage group computed by GMendel.  The 'print lod' command will print
the LOD scores between all pairs of loci in a particular group.
Without specifying any groups the command will print a table of LOD
scores for each group.  Tables can be printed for specific groups, for
example 2 and 5, using the command 'print lod 2 5'. If there is more
than one population, the pooled LOD scores for each pair of loci are
printed.
*/
#define HELP_REVERSE 50
/* reverse
The order of one or more linkage groups can be reversed with the
reverse command. Using the reverse command without specifying a list
of groups will reverse each group. One or more groups can be specified
by adding a list of group numbers to the end of the reverse command.
*/
#define HELP_JOIN 51
/* join
The join command merges two linkage groups and has the form 'join 5
3'. In this case the loci in group 3 would be added to the end of the
loci in group 5. Group 3 remains unchanged.
*/
#define HELP_MAKE_ASCII_PROFILE 52
/* make ar
The command 'make ar' (make ascii r profile) is used to look for
multiple 'true' linkage groups in a single linkage group as computed
by GMendel. When a group has been ordered, we expect that for a
particular locus the recombination frequency will monotonically
increase as we consider loci further from the first locus in the
ordering. GMendel displays this visually by creating one graph for
each locus in the linkage group. The graph plots the loci in the
computed order versus the recombination frequency of that locus with
the locus being considered in the plot.  It is expected that the
recombination frequencies will monotonically decrease to zero (the
recombination frequency between a locus and itself is zero) and then
monotonically increase. In practice, the decrease and increase are not
monotonic, but reasonably close.
*/
#define HELP_MAKE_PROFILE 53
/* make pr
See 'make ar'. The command 'make pr' (make profile for r) creates a
file that can be loaded into gnuplot and then examined graphically one
frame at a time.
*/
#define HELP_FOLD 54
/* fold
There are some situations (the phase is specified incorrectly) where
the r values that GMendel computes will be much larger than 0.5. If
the reason the value is larger than 0.5 is that the phase is wrong,
the actual r value will be 1.0 - r. The incorrect phase usually only
affects the r value and not the LOD score. An exception to this is the
mixed phase complex matings.  The 'fold' option allows you to specify
that significant r values larger than 0.5 should be replaced with 1.0
- r. The default is to not fold r values.
*/
#define HELP_LOAD_DATA 55
/* load data
The 'load data <filename>' command is used to load a data file into
GMendel. The format of the data file is discussed in the manual. The
'load data' command causes data currently in GMendel to be discarded.
*/
#define HELP_LOAD_EXPECTATION 56
/* load expectation
GMendel has predefined expected segregation ratios for all of the
standard mating types. Users can define "complex" mating types and
then use the 'load expectation <filename>' command to read them into
GMendel.
*/
#define HELP_EXPERIMENTAL 57
/* x
The command 'x' (for experimental) is not intended to be used. The
results of using the 'x' command are undefined.
*/
#define HELP_VIEW_PROFILE 58
/* view profile
See 'make ar'. The 'view profile' command displays the r value profile
of a linkage group on the screen. This command requires that you be
able to run the gnuplot program on your Xterminal.
*/
#define HELP_VIEW_LOD 59
/* view plod
See 'make al'. The 'view plod' command displays the LOD value profile
of a linkage group on the screen. This command requires that you be
ablt to run the gnuplot program on your Xterminal.
*/
#define HELP_GROUP_VIEW_ORDER 60
/* view group
See 'print postscript'. The 'view group' command displays the
postscript map of a linkage group on your Xterminal using the program
gnuplot.
*/
#define HELP_MAKE_ASCII_PROFILE_LOD 61
/* make al
The command 'make al' (make ascii LOD profile) is used to look for
multiple 'true' linkage groups in a single linkage group as computed
by GMendel. When a group has been ordered, we expect that for a
particular locus the LOD scores will monotonically decrease as we
consider loci further from the first locus in the ordering. GMendel
displays this visually by creating one graph for each locus in the
linkage group. The graph plots the loci in the computed order versus
the LOD score of that locus with the locus being considered in the
plot.  It is expected that the LOD scores will monotonically increase
(the LOD score between a locus and itself is set to the maximum
observed LOD) and then monotonically decrease. In practice, the
increase and decrease are not monotonic, but reasonably close.
*/
#define HELP_MAKE_PROFILE_LOD 62
/* make pl
See 'make al'. The command 'make pl' (make profile for LOD) creates a
file that can be loaded into gnuplot and then examined graphically one
frame at a time.
*/
#define HELP_WIDTH 63
/* width
The 'make ar' (make ascii r profile) and 'make al' (make ascii LOD
profile) commands produce output for windows of a specified width and
height. The command 'set width <n>' sets the width of the window to
<n> characters.
*/
#define HELP_HEIGHT 64
/* height
The 'make ar' (make ascii r profile) and 'make al' (make ascii LOD
profile) commands produce output for windows of a specified width and
height. The command 'set height <n>' sets the height of the window to
<n> lines.
*/
#define HELP_PSADD 65
/* psadd
GMendel will produce two types of postscript maps, one using
recombination frequencies between adjacent loci and the second using
the distance between each locus and the first locus. The distance is
computed using the sum of distances between adjacent loci.
*/
#define HELP_SUBGROUP 66
/* subgroup
When analyzing complex data, some matings may not be informative
requiring the recombination frequency to be estimated. The 'set
subgroup <mating type list>' command is used to examine the subset of
the data with a mating type in <mating type list>'.
*/
#define HELP_SIGNIFICANCE 67
/* significance
Several of the print commands mark values as being significant with a
'*'. The level of significance can be set using the 'set sig <value>'
where <value> might be 0.01, 0.05, 0.001, or any value that is
desired.
*/
#define HELP_PRINT_INTERORDER 68
/* print interorder
The 'print interorder' command prints a report with a number of
statistics for adjacent loci in the computed order The statistics
printed are r, variance or r, standard error of r, LOD score, G for
linkage, and the significance of the G score.
*/
#define HELP_PRINT_GGROUP 69
/* print ggroup
The 'print ggroup <group list>' command will print the G linkage value
and it significance for all pairs of loci in a group. If <group list>
is one or more group numbers, a table is produced for each group. If
<group list> is empty, a table is produced for each group.
*/
#define HELP_PRINT_GORDER 70
/* print gorder
The 'print gorder <group list>' command will print the G total, G
pooled and G heterogenaity statistics for the pooled data and the G
linkage for each of the populations. These statistics are printed for
each pair of adjacent loci in the group.
*/
#define HELP_PRINT_GPORDER 71
/* print gporder
The 'print gporder <group list>' command will print the G total, G
pooled and G heterogenaity statistics for the pooled data and the G
linkage for each of the populations. Associated with each G statistic
is the significance of the G statistic. These statistics are printed
for each pair of adjacent loci in the group.
*/
#define HELP_PRINT_CROSSOVERS 72
/* print crossovers
The phenotype data is printed with loci in order using the 'print
crossovers <group list> command. Viewing the data this way can help
identify the position of the crossovers that occurred.
*/
#define HELP_PRINT_VARIANCE 73
/* print variance
The 'print variance <group list>' command will print the variance of
the recombination frequency for each pair of loci in a group.
*/
#define HELP_PRINT_PERCENT 74
/* print percent
The percent of the recombination frequencies that could not be
computed directly from the data and had to be estimated is printed
using the 'print percent' command.
*/
#define HELP_PRINT_DISTRIBUTION 75
/* print distribution
The 'print distribution <locus1> <locus2>' command will print a table
of observed phenotypes of locus1 and locus2.
*/
#define HELP_FUNCTION 76
/* function
There are four functions that can be used to evaluate an ordering of
the loci. The selected function is used to find the ordering that
minimizes the the value of the function. The simplest, and fastest,
function is the sum of adjacent recombination frequiencies or SAR.
This function is selected by the 'set function sar' command. A
generalization of the SAR function, the kSAR function, takes longer to
evaluate, but will produce good ordering of large groups with many
fewer order evaluations. The kSAR function is selected with the 'set
function ksar' command. Another generalization of the SAR function is
the gsar function selecte with the 'set function gsar' command. The
fourth function minimizes the discrepancies between all possible r
values. This function takes the longest time to evaluate and is
selected with the 'set function chi' command. Details for each of
these functions are available with the 'help sar' or 'help gsar' or
...  commands.
*/
#define HELP_MONTE 77
/* monte
The 'monte' carlo function is used to estimate the robustness of a
linkage map by repeatedly computing the order of the loci. If there
are several linkage maps that are each nearly as likely, we will see
different locus orders each time we compute the linkage map. The Monte
Carlo function will record the position of each locus in each of the
linkage maps that is computed. The number of times to compute the
linkage map is controled by the 'set boot n' command where n is the
number of times to compute the map. The default value for n is 25.
With this data it is possible to see the mean position and variance of
each locus using the 'print boot' command. The 'print bh' command will
print a histogram for each locus indicating the frequency of the locus
at each position on the map. Using the 'monte' command with no
arguments will gather the monte carlo statistics for each group. To
compute the monte carlo statistics for groups 2, 3 and 5, use the
'monte 2 3 5' command.
*/
#define HELP_BOOT 78
/* boot
The 'bootstrap' function is used to estimate the robustness of a
linkage map by randomly selecting n individuals with replacement from
the population, computing the recombination frequencies from the
selected data and then computing the order of the loci. The process of
selecting individuals and computing a map is repeated many times. If
there are several linkage maps that are each nearly as likely or the
choice of individuals from the population influences the order, we
will see different locus orders each time we compute the linkage
map. The Monte Carlo function will record the position of each locus
in each of the linkage maps that is computed. The number of times to
compute the linkage map is controled by the 'set boot n' command where
n is the number of times to compute the map. The default value for n
is 25.  With this data it is possible to see the mean position and
variance of each locus using the 'print boot' command. The 'print bh'
command will print a histogram for each locus indicating the frequency
of the locus at each position on the map. Using the 'boot' command
with no arguments will gather the bootstrap statistics for each
group. To compute the bootstrap statistics for groups 2, 3 and 5, use
the 'monte 2 3 5' command.
*/
#define HELP_PRINT_BOOT 79
/* print boot
The 'print boot' command can be used after the Monte Carlo statistics
or the bootstrap statistics have been collected (see 'monte' and
'boot'). The 'print boot' command will produce a table of the mean
position, variance and standard error for each locus. The table is
ordered by the mean position of each locus. At the bottom of the table
is the mean SAR score for each ordering, and its variance and standard
error. To print the table for groups 2, 3 and 5, use the 'print boot 2
3 5' command.
*/
#define HELP_PRINT_BH 80
/* print bh
The 'print bh' command can be used after the Monte Carlo statistics or
the bootstrap statistics have been collected (see 'monte' and 'boot').
The 'print bh' command will produce a histogram for each locus in the
linkage group that shows the frequency that the locus appeared in each
position of the various locus orderings. Each "X" in a bar of the
histogram represents 10 percent and a digit n represents n percent.

	3
This 	X    indicated 23 percent of the time, the locus appeard at 
	X    position 6.
      _____
      45678

To print a set of histograms for linkage groups 2, 3 and 5, use the
'print bh 2 3 5' command.
*/