# read BSR output and assign aliases to the two query genomes ("Cm", "Cp")
new load_bsr1 load-bsr heightf=0,bsr-file=./Cc_GPIC_Cm_Nigg_Cp_AR39.txt,genome1=Cm,genome2=Cp

# draw ruler/coordinates
coords

tiny-cgap
genes
# highlight conserved hypotheticals
new HCH rectangle feat-type=CDS,feat-tag=product,feat-tag-regex=hypothetical\sprotein,innerf=same,outerf=same,opacity=0.8,color1=#00ff00
medium-label label-text=all genes / green:hypothetical proteins
small-cgap

# genes that are present in all 3 genomes
new CH1 rectangle color1=none,color2=#000000,heightf=0.14,feat-type=contig
tiny-cgap outerf=same
new bsr_all bsr 0.07 threshold=0.4,genomes=Cm|Cp,signature=11,color1=#a0a0a0,color2=#a0a0a0
# genes that are unique to the reference
new bsr_ref bsr 0.07 threshold=0.4,genomes=Cm|Cp,signature=00,color1=#f91919,color2=#f91919,innerf=same
medium-label label-text=grey:conserved in all 3 / red:unique to C. caviae GPIC
medium-cgap

# genes that are present only in the reference and Chlamydophila pneumoniae AR39
new CH1 rectangle color1=none,color2=#000000,heightf=0.14,feat-type=contig
tiny-cgap outerf=same
new bsr_cp bsr 0.07 threshold=0.4,genomes=Cm|Cp,signature=01,color1=#c411be,color2=#c411be
medium-label label-text=ONLY found in C. caviae GPIC and C. pneumoniae AR39m
medium-cgap

# genes that are present only in the reference and Chlamydia muridarum Nigg
new CH2 rectangle color1=none,color2=#000000,heightf=0.14,feat-type=contig
tiny-cgap outerf=same
new bsr_cm bsr 0.07 threshold=0.4,genomes=Cm|Cp,signature=10,color1=#1511c4,color2=#1511c4
medium-label label-text=ONLY found in C. caviae GPIC and C. muridarum Nigg

# caption
large-label innerf=0,label-text=C. caviae GPIC,label-type=horizontal,font-style=italic