I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format:
/Applications/Mauve.app/Contents/MacOS/progressiveMauve ref1.fa ref2.fa --output alignment.xmfa
I then open the xmfa file in the Mauve GUI and export the SNPs. Is there a way of doing this using a command? I have tried to follow the procedure described here but the link to snapshot releases of Mauve does not work anymore.
I could not find anything in the Mauve command line help:
nor on the Mauve website.
I tried the procedure described by Konrad Rudolph. I wrote:
in the terminal. Is this correct? Don't I need an export and quotation marks to create a bash variable? I tried adding an export and using quotation marks for the file but the error below remained the same.
export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"
java org.gel.mauve.analysis.SnpExporter -f alignment.xmfa -o aln.snps
and it seems to work.