diff --git a/examples/DisappearingMicrobiome/run.sh b/examples/DisappearingMicrobiome/run.sh
index 7bd707a..677bad4 100755
--- a/examples/DisappearingMicrobiome/run.sh
+++ b/examples/DisappearingMicrobiome/run.sh
@@ -3,53 +3,53 @@
 cp annot.txt annot3.txt
 
 # De Filippo
-for l in `cat genomes.all.txt | grep g__Prevotella  | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Xylanibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Treponema | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Butyrivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Prevotella  | cut -f 1 | sed -n '0~4p'` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Xylanibacter | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Treponema | cut -f 1 | sed -n '0~4p'` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Butyrivibrio | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
 
 # Yatsunenko
-for l in `cat genomes.all.txt | grep s__Streptococcus_alactolyticus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Clostridium.s__leptum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep s__Clostridium_orbiscindens | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep s__Clostridium_innocuum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep s__Streptococcus_alactolyticus | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Clostridium.s__leptum | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep s__Clostridium_orbiscindens | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep s__Clostridium_innocuum | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
 
-for l in `cat genomes.all.txt | grep g__Lactobacillus.s__ruminis | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Eubacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Dialister | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Oscillospira | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Lactobacillus.s__ruminis | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Eubacterium | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Dialister | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Oscillospira | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
 
 # Clemente
-for l in `cat genomes.all.txt | grep g__Helicobacter | cut -f 1 | sed -n '0~6p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Phascolarctobacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Paraprevotella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Anaeroplasma | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Bulleidia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Helicobacter | cut -f 1 | sed -n '0~6p'` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Phascolarctobacterium | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Paraprevotella | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Anaeroplasma | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Bulleidia | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
 
-for l in `cat genomes.all.txt | grep g__Coprococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Coprococcus | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
 
 #Martinez
-for l in `cat genomes.all.txt | grep g__Weissella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Slackia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Streptococcus | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Weissella | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Slackia | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Streptococcus | cut -f 1 | sed -n '0~14p'` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
 
-for l in `cat genomes.all.txt | grep g__Gordonibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Odoribacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Gordonibacter | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Odoribacter | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
 
 
 # Obregon
-for l in `cat genomes.all.txt | grep g__Succinivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Catenibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Succinivibrio | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Catenibacterium | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
 
-for l in `cat genomes.all.txt | grep g__Dorea | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Blautia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Dorea | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Blautia | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
 
 
-for l in `cat genomes.all.txt | grep g__Bacteroides | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Faecalibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
-for l in `cat genomes.all.txt | grep g__Ruminococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Bacteroides | cut -f 1 | sed -n '0~14p'` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Faecalibacterium | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
+for l in `cat genomes.all.txt | grep g__Ruminococcus | cut -f 1` ; do echo -e $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
 
 
 graphlan_annotate.py DisMic.xml DisMic.annot.xml --annot annot3.txt