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This example config file is preconfigured for using NCBI blast with soft masking. Input files will be searched in subdirectory "plastids", output will be written in files blastout.zip (original blast output), cgviz.zip (internal format suitable for Matches2Distances) and lengths.zip (containing length information of the corresponding genomes).

### GBDPblaster Inifile

### here one can select the alignment tool to use.
localAlignmentTool=NCBIBlastWrapper
#localAlignmentTool=WUBlastWrapper
#localAlignmentTool=BlastZWrapper


############################# NCBI BLAST Options ##############################

### paths of the NCBI blast executables
NCBIBlastWrapper.appPath=blastall
NCBIBlastWrapper.formatDbPath=formatdb

### additional command line options
#NCBIBlastWrapper.additionalOptions=
#NCBIBlastWrapper.wordLength=7

### blast low complexity filter
### 0/disable, 1/enable the low complexity filter
#NCBIBlastWrapper.lowComplexityFilter=1
NCBIBlastWrapper.lowComplexityFilter=0

### use soft masking
NCBIBlastWrapper.softMasking=1


############################# WU BLAST Options ################################

WUBlastWrapper.appPath=wu-blast
WUBlastWrapper.lowComplexityFilter=1
WUBlastWrapper.softMasking=1
#WUBlastWrapper.wordLength=7
#WUBlastWrapper.additionalOptions=matrix=pupy


############################# BLASTZ Options ##################################

BlastZWrapper.appPath=blastz

printCmdLine=1

############################# Common Options ##################################

### 1=use tblastx, default: 0
#translateNucleotides=1

### number of jobs to start in parallel
parallelJobCount=1
#parallelJobCount=2

### eValue threshold
#eValueThreshold=1E-3
eValueThreshold=10


############################# I/O Options #####################################

### directory containing the genomes
genomesDir=./plastids
genomesExt=.fasta

### BLAST Output directory / zipfile
#blastOutputDir=./blastout
blastOutputDir=./blastout.zip

### CGVIZ Output directory / zipfile
#outputDir=./cgviz
outputDir=./cgviz.zip

### CGVIZ Length files output directory / zipfile
filesLengthDir=lengths.zip