Main tool : mummer
Additional tools:
- fig2dev (3.2.3)
- gnuplot (4.0)
- xfig (3.2)
MUMmer is a versatile alignment tool for DNA and protein sequences.
Better documentation for Mummer can be found at https://github.com/mummer4/mummer
A tutorial can be found at https://mummer4.github.io/tutorial/tutorial.html
And the manual can be found at http://mummer.sourceforge.net/manual/
mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums
mummerplot -x "[0,275287]" -y "[0,265111]" --terminal png -postscript -p mummer mummer.mums
nucmer -c 100 -p nucmer B_anthracis_Mslice.fasta B_anthracis_contigs.fasta
show-snps -C nucmer.delta > nucmer.snp
promer -p promer_100 -c 100 H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta
mummerplot -l nucmer.delta -p test_mummer_plot --png
gnuplot test_mummer_plot.gp