;Parsnp configuration File
;
[Reference]
file=/home/ben/git/coverm/tests/data/2_single_species_dummy_dataset/2genomes/P_2019_08_07_124012687151/2genomes_different_lengths.genome1.fasta.ref
reverse=0
[Query]
file1=genomes/2genomes_different_lengths.genome2.fasta
reverse1=0
file2=genomes/2genomes_different_lengths.genome1_duplicate.fasta
reverse2=0
[MUM]
anchors=1.0*(Log(S))
anchorfile=
anchorsonly=0
calcmumi=0
mums=1.1*(Log(S))
mumfile=
filter=1
factor=2.0
extendmums=0
[LCB]
recombfilter=0
cores=32
diagdiff=0.12
doalign=2
c=21
d=300
q=30
p=15000000
icr=0
unaligned=0
[Output]
outdir=/home/ben/git/coverm/tests/data/2_single_species_dummy_dataset/2genomes/P_2019_08_07_124012687151
prefix=parsnp
showbps=1

