Quick Start

The following section illustrates some of the major commands of CARTHAGENE on small example data sets. This quick start example is done using the shell interface but can also be performed using the graphical interface (either by clicking buttons in most cases, sometimes by issuing the command in the text window). For this QuickStart, we just give here a fast description of CARTHAGENE's main principles, you'll find more information in the sequel of the Documentation.

• Handling Data Sets:
  • Data sets are loaded from files formated as in MapMaker.
  • The current data set used by CarthaGene to compute maps, is always the last data set which has been ``created'' (loaded or merged).
  • The merging operators (dsmergen, dsmergor) accept only two data sets. You will have to call them several times to merge more than two data sets.
  • A list of implicitely selected loci is always active. By default this list contains all the markers of the last data set created (loaded or merged). The user can change this selection of loci (mrkselset) if he wants to build maps with a specific selection of loci.

• Map Search:
  • Each ordering algorithm sends the maps it has computed to a specific storage area called ``the heap''.
  • The so-called ``heuristics'' algorithms start from the data sets and compute maps from scratch..
  • The so-called ``Local Search'' algorithms, and the verification algorithms start from the best map on the heap and try to improve this map.

• Results exploitation and storage:
  • CarthaGene considers that the result of a map search is the set of the $k$ best maps found during the session,
  • The heap always keep these $k$ best solutions.
  • if the hierarchy of data sets changes, the heap becomes obsolete and is emptied.

To start CARTHAGENE shell, run the shell of Tcl (tclsh). If CARTHAGENE is well installed, its functionalities should be available and a message mentioning that CarthaGene has been loaded should appear (the prompt might not be the same, don't worry). Under windows, you can use the graphical interface and directly type your command in the main window.

[alta:exemple] tclsh

   CarthaGene version 0.999-LKH, Copyright (c) 1997-2004 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY. 
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

CG>

If you type help, the complete list of the commands of CarthaGene will appear.

CG> help
CartaGene commands :
====================
miscellaneous :
---------------
cgout           Save the output to a file.
cgtolerance     Sets EM convergence thresholds.
cgversion       Get the version.
cgrestart       Reset the application.
cgstop          To stop a running command, type ctrl-c.
cglicense       Deprecated command.
cgstat          Get some performance information.
cgnotrobust     Disable reliability test of framework maps.
cg2tsp          Convert current marker selection to TSP.
cgrobustness    Sets reliability threshold for framework maps.
cgsave
cgexport

to manipulate data sets :
-------------------------
dsload          Load a Biological Data Set.
dsmergor        Merge by order two Biological Data Sets.
dsinfo          Summarize the current data sets.
dsmergen        Merge two Biological Data Sets.
dsget           Get a list of the current data sets description.

to manipulate groups :
----------------------
group           Identify linkage groups.
groupget        Get a group by markers ID.

to manipulate loci :
--------------------
mrklod2p        Print the two points LOD matrix.
mrkname         Get the name of a locus.
mrkselget       Return the loci selection into a list.
mrkid           Get the integer id of a locus.
mrkallget       Return all the loci into a list.
mrkfr2p         Print the two points FR/Breaks matrix.
mrklast         Get the integer id of the last known locus.
mrkselset       Set the marker list(by Id).
mrkdist2p       Print the two points distance matrix.
mrkmerge        Merges two compatible markers.
mrkdouble       Identifies pairs of markers with compatible typing.
mrkinfo         Tell which data set each marker belongs to.
mrkmerget       Retrive a list of merged markers.

to manipulate the heap :
------------------------
heapsizeget     get the size of the heap.
heapsize        Resize the heap.
heapget         Get the heap, in a list.
heaprintd       Display the heap in detail, sorted.
heaprint        Display the heap sorted.
heaprinto       Display the heap of maps by privileging the order of the ma...
heapequiset     enable or disable the equivalence mode of the heap.
heaprintg       Draw the heap(current best maps) into a graphical display.

to manipulate a map :
---------------------
maprint         Print a map.
mapordget       Get a order of loci from a map, in a list.
mapocb          Obligate Chromosome Breaks of a map.
maprintdr       Print a map reverse, in detail.
mapget          Get a map, in a list.
maprintd        Print a map, in detail.

to search for good maps :
-------------------------
greedy          Find good maps using the greedy algorithm.
lkhocbn         Provide a (nice) map, using normalized 2-points Obligate Ch...
ilkhl           Provide a (nice) map, using dynamically updated 2-points LO...
mfmapd          Provide quickly a (nice) map, using the 2-points distances.
buildfw         Build a framework map.
ilkhn           Provide a (nice) map, using dynamically updated normalized ...
mfmapl          Provide quickly a (nice) map, using the 2-points LOD criteria.
algogen         Find good maps using the genetic algorithm.
flips           Try to improve the best map by flipping.
ilkhocb         Provide a (nice) map, using dynamically updated 2-points Ob...
lkh             Provide a (nice) map, using 2-points loglikelihoods and Lin...
ilkh            Provide a (nice) map, using dynamically updated 2-points lo...
quietset        Make the search process quiet.
sem             Compute a Single map (Single EM).
polishtest      Try to improve the map giving with markers by polishing.
nicemapd        Provide quickly a (nice) map, using the 2-points distances.
ilkhocbn        Provide a (nice) map, using dynamically updated normalized ...
annealing       Find good maps using the annealing algorithm.
nicemapl        Provide quickly a (nice) map, using the 2-points LOD criteria.
verbset         Make the search process verbose.
lkhd            Provide a (nice) map, using 2-points distances and Lin-Kern...
polish          Try to improve the best map by polishing.
build           Build maps with two-points informations.
lkhl            Provide a (nice) map, using 2-points LOD criteria and Lin-K...
lkhocb          Provide a (nice) map, using 2-points Obligate Chromosome Br...
ilkhd           Provide a (nice) map, using dynamically updated 2-points di...
lkhn            Provide a (nice) map, using normalized 2-points loglikeliho...

Type '<command-name> -H' for more help with a particular command.
Some commands have a default behaviour :
Type 'd_<command-name>' to use it.
To change the defaults, edit the '.tclshrc'