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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.
best maps found during the session,
best solutions.
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.
CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (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> help CartaGene commands : ==================== miscellaneous : --------------- cgout Save the output to a file. cgprecision Controls the number of digits printed for estimated distances. cg2pt Compute approximated likelihoods based on 2-point estimatio... cgtolerance Sets EM convergence thresholds. cgversion Get the . 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 Save the state of the current session. cgexport Save the state of the current session. to manipulate data sets : ------------------------- dsclone Clone a dataset. dsbp Compute the number of breakpoints between one order data se... dsload Load a Biological Data Set. dsrhconv Convert a radiated hybrid dataset into haploid|diploid|error. dsbplambda Replaces the traditional criterion by the comparative mappi... dsmergor Merge by order two Biological Data Sets. dsbpcoef Modifies the coefficient factor value applied to the number... 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 : -------------------- mrkdoubleget Retrive a list of pairs of markers with compatible typing. 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. bestprint Print the best map in the heap. bestprintd Print the best map in the heap, in detail. to manipulate a map : --------------------- maprint Print a map. mapordget Get a order of loci from a map, in a list. mapbp Compute the number of breakpoints between one order data se... mapocb Compute the number of 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. imputation Impute corrected genotypes according to the error model (on... verbset Make the search process verbose. lkhd Provide a (nice) map, using 2-points distances and Lin-Kern... errorestimation Based on the current marker order, estimate the error rate ... polish Try to improve the best map by polishing. build Build maps with two-points informations. lkhocb Provide a (nice) map, using 2-points Obligate Chromosome Br... lkhl Provide a (nice) map, using 2-points LOD criteria and Lin-K... ilkhd Provide a (nice) map, using dynamically updated 2-points di... lkhn Provide a (nice) map, using normalized 2-points loglikeliho... comparative mapping : --------------------- paretoplotg Draw the Pareto frontier. paretosave Save the pareto frontier. paretobestprint Print the best map in the Pareto frontier. paretobestprintd Print the best map in the Pareto frontier, in detail. paretogreedy Improve a Pareto frontier approximation. paretoinfog Internal command. paretoheapsize Set the heap size used by pareto functions. paretogreedyr Improve a selection of the Pareto frontier approximation. paretolkhn Provide a Pareto frontier approximation. paretolkh Provide a Pareto frontier approximation. paretoinfo Display the Pareto frontier. dsbp Compute the number of breakpoints between one order data se... dsbplambda Replaces the traditional criterion by the comparative mappi... dsbpcoef Modifies the coefficient factor value applied to the number... mapbp Compute the number of breakpoints between one order data se... graphical commands : -------------------- maprintg Draw a map into a graphical display. heaprintg Draw the heap(current best maps) into a graphical display. paretoplotg Draw the Pareto frontier. 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 '.carthagenerc'