SizeDiv | size diversity: (- sum of p * log(p)), where p is the                      proportion of all adult cells in the soup that fall in                      a size class.            AgeSize | average age of sizes: whenever a new size class appears                      or reappears, its age starts counting at zero.  At each                      instant of time, the age of all size classes is summed                      and divided by the number of size classes.            NumGeno | number of genotypes: total number of distinct genotype                      classes of adult cells living in the soup.            GenoDiv | genotype diversity: (- sum of p * log(p)), where p is the                      proportion of all adult cells in the soup that fall in                      a genotype class.            AgeGeno | average age of genotypes: whenever a new genotype class                      appears or reappears, its age starts counting at zero.                      At each instant of time, the age of all genotype classes                      is summed and divided by the number of size classes. data file = divdat.1     This is the name of the file containing the diversity indicesoutput by the Diverse program.  In long runs, a series of these files may beproduced, with the names divdat.1, divdat.2, divdat.3, ..., divdat.X.  TheDiversity option will read each of them in turn, if you specify the name ofthe first one. range file = divrange     This is the name of the file containing the ranges of the diversityindices, output by the Diverse program. shrink factor      = 1     The axes will normally fill the whole screen, but if you use a shrinkfactor of less than 1, the y axis will shrink to fill only part of the screen.This option was introduced to get the display to fit a device that wascropping the vertical dimension (when making a video tape).====== TEMPLATE ============================================================     This option provides a display of the structure of a genome, asindicated by the arrangement of instructions using templates.  Since allinstructions that affect the control flow of the program (jump, call) usetemplates, this provides a sort of schematic of the program structure.The Template option will read and display genomes from the genebank.You will need to know what genome are stored there.  Use the arg t optionto get a list of the genomes stored in any of the .gen files in the genebank:e.g.:  arg t 0080.genwill produce a list of the genotypes in the 80 size class in the 0080.genfile.     Selecting the Template option generates a window that looks like this:+templates--------------------------+| genebank path = c:\tierra\gb      || genefile name = 0080.gen          || genotype      = aaa               || min temp size = 3                 |+-----------------------------------+     Within this window, use the cursor key to move to an option, then typein your choice.  When you have all the options as you want them, use Ctrl-Enterto activate the Template display.  Use the Escape key to exit from theTemplate option.     An explanation of the Template options follows: genebank path = c:\tierra\gb     This is the path to the genebank, where the files containing the savedgenomes of the creatures are written by the Tierra program (XXXX.gen,XXXX.tmp, XXXX.mem files). genefile name = 0080.gen     This is the name of the file in the genebank containing the genomes ofthe size that you want to examine. genotype      = aaa     This is the actual genotype name of the creature that you want to examine,of the size indicated by the name of the genefile. min temp size = 3     You might want to ignore templates below a certain size.  There is aMinTemplSize parameter in the soup_in file used by the Tierra simulator.Templates below this size are not recognized as templates.  You should setmin temp size to the same value as was set in the soup_in file of the runthat produced the genome you are examining.     When you run the Template program by hitting Ctrl-Enter, you will geta window that looks like this (for 0080aaa):        +-------------------------+        | locus:   9, adrb  0000  |        | locus:  16, adrf  0001  |        | locus:  28, call  0011  |        | locus:  34,  jmp  0010  |        | locus:  54,  jmp  0100  |        | locus:  61,  jmp  0101  |        +-------------------------+     The second column (numbers) contains the position in the genome of theinstructions using templates.  The third column contains the names of theinstructions at those positions that use the templates.  The fourth columncontains the actual templates used by the instructions at those positions.====== PROBE ===============================================================     This option allows you to compare two genomes by probing the sequence ofone with the sequence of the other.  Probe slides the probe sequence alongthe genome sequence and determines the positions of the major alignments.These alignments are then reported to you, and you may choose how many youwant to recognize.  Then the two genomes are displayed together, in theiralignments, with the differences highlighted.  The Probe program makes aheroic effort to deal with complications like multiple allignments, insertionsand deletions, and overlaping alignments.  However, it fails miserably forsome of the more complicated cases (the ability to detect insertions ordeletions may not be working).  This program is not mature, but itprovides some help in comparing sequences.          The Probe option will read and display genomes from the genebank.You will need to know what genome are stored there.  Use the arg t optionto get a list of the genomes stored in any of the .gen files in the genebank:e.g.:  arg t 0080.gene.g.:  arg t 0045.genwill produce a list of the genotypes in the 80 size class in the 0080.genfile, and in the 45 size class in the 0045.gen file.     Selecting the Probe option generates a window that looks like this:+probe----------------------------+| genome path = c:\tierra\gb      || genome file = 0080.gen          || genome      = aaa               || probe path = c:\tierra\gb       || probe file = 0045.gen           || probe      = aaa                |+---------------------------------+     Within this window, use the cursor key to move to an option, then typein your choice.  When you have all the options as you want them, use Ctrl-Enterto activate the Probe display.  Use the Escape key to exit from theProbe option.     An explanation of the Probe options follows: genome path = c:\tierra\gb     This is the path to the genebank, where the files containing the savedgenomes of the creatures are written by the Tierra program (XXXX.gen,XXXX.tmp, XXXX.mem files). genome file = 0080.gen     This is the name of the file in the genebank containing the genomes ofthe size that you want to examine. genome      = aaa     This is the actual genotype name of the creature that you want to compareto the probe, of the size indicated by the name of the genome file. probe path = c:\tierra\gb     This is the path to the genebank, where the files containing the savedgenomes of the creatures are written by the Tierra program (XXXX.gen,XXXX.tmp, XXXX.mem files). probe file = 0080.gen     This is the name of the file in the genebank containing the genomes ofthe size that you want to examine. probe      = aaa     This is the actual genotype name of the probe that you want to slidealong the genome indicated by the first three options, (size indicated by thename of the probe file).     When you run the Probe program by hitting Ctrl-Enter, you will geta window that looks like this (for 0080aaa and 0045aaa):        +----------------------------------------------+        | position:  0   fit: 44   diff: 0   idpos: 0  |        | position: -1   fit: 16   diff: 0   idpos: 0  |        | position:  1   fit: 14   diff: 0   idpos: 0  |        | position: 25   fit: 13   diff: 0   idpos: 0  |        | position: 23   fit: 12   diff: 0   idpos: 0  |        | position:  7   fit: 11   diff: 0   idpos: 0  |        +----------------------------------------------+     The first pair of columns (positon) contains the relative position of thealignments of the two genomes.  0 indicates that the alignment occurred withthe first instruction of the two genomes together, -1 indicates that the firstinstruction of the genome is aligned with the second instructions of the probe,1 indicates that the first instruction of the probe is aligned with thesecond instruction of the genome.     The second pair of columns (fit) contains the goodness of fit, as thenumber of instructions that matched between the genome and probe in thatalignment.  In this example, the probe is 45 instructions long, so a matchof 44 indicates that only one instruction is diferent between the probe andgenome.       The third pair of columns (diff) indicates a difference in lengthresulting from an insertion (positive) or deletion (negative).     The fourth pair of columns (idpos) indicates the position of theinsertion of deletion.     When this window appears, you examine the alignments to decide how manyyou want to use.  In this case, there is only one really good alignment, sowe will use one.  Now hit Esc, and another window will appear that lookslike this:                                           +number of matches to use-----+                                           | number of matches = 1       |                                           +-----------------------------+     You either accept the suggested value (1) or change it, the hitCtrl-Enter, and the alignments will be displayed in two windows that looklike this:+instruction list--------------------------------------------------------------+|   0:nop_0  1:nop_1  2:or1    3:shl    4:zero   5:if_cz  6:sub_ab 7:sub_ac    ||   8:inc_a  9:inc_b  a:dec_c  b:inc_c  c:pushax d:pushbx e:pushcx f:pushdx    ||   g:pop_ax h:pop_bx i:pop_cx j:pop_dx k:jmp    l:jmpb   m:call   n:ret       ||   o:mov_cd p:mov_ab q:moviab r:adr    s:adrb   t:adrf   u:mal    v:divide    |+------------------------------------------------------------------------------++genome-to-probe match:  genome (top) - 0080aaa    probe - 0045aaa ------------+| 11114233os00007pt0001861101um0011vk001051100cde1010qa5k010089k010151011ihgn1 || 11114233os00007pt0001861101um0011vk001051110c                                ||                                                                              || 1105                                                                         ||                                                                              |+------------------------------------------------------------------------------+     The highlighting is not indicated above, but it indicates where the twogenomes do not match.====== PREPARE - FRAGMENT ===================================================     If you want to display a portion of a long run, you may edit the longrun using the "Prepare - Fragment" option from the Beagle menu, or thestand-alone fragment utility.  This will produce an output file which maybe read by itself, or you may produce several fragments, and then concatenatethem together in order to produce an edited version of a longer run.  Theedited fragment(s) resulting from this process MUST be used as the input fileoperated on by the "Prepare - Run Info" option to produce the run_info filesread by the Bars and Trace displays.  Beware that if the fragments begin orend at the same time that the "update" attempts to create a new list, very badinteractions can result.  Just be sure you don't try to fragment and update atthe same time (if you use the default update frequency of 100, don't breakyour fragments at 100 million marks).   select the Prepare option   then select the Fragment option     Selecting the "Prepare - Fragment" option will produce a window thatlooks like this:+fragment----------------------------------+| directory    = c:\tierra\td              || input file   = break.1                   || output file  = fragment.run              || start time   = 0                         || stop time    = 1                         |+------------------------------------------+     Within this window, use the cursor key to move to an option, then typein your choice.  When you have all the options as you want them, use Ctrl-Enterto activate the "Prepare - Fragment" process.  Use the Escape key to exit fromthe window.     An explanation of these "Prepare - Fragment" options follows: directory  = c:\tierra\td     This is the path to the file containing the birth and death recordsoutput by the Tierra program (the break.X files). input file = break.1     This is the name of the file containing the birth and death recordsoutput by the Tierra program.  In long runs, a series of these files may beproduced, with the names break.1, break.2, break.3, ..., break.X.  ThePrepare - Fragment program will read each of them in turn, if you specify thename of the first one. output file  = fragment.run     This is the name of the fragmentary output file that will be produced. start time   = 0     This is the start time of the fragment that you wish to produce, inmillions of instructions. stop time    = 1     This is the stop time of the fragment that you wish to produce, inmillions of instructions.  Be sure the start and stop times do not coincidewith update times.  The stop time must be greater than the start time.     The "Prepare - Fragment" option uses a lot of memory.  On long runs,it may run out of memory.  If this happens, you should use the stand-alonefragment tool.  It takes the same input parameters, but by not being bundledwith the rest of the Beagle tools, it has a lot more memory to spare.  Justtype fragment the DOS prompt.