branch_color_from_ancestor	0
title	A maximal core gene for clade Y
title_font_size	11
annotation_background_offset	-0.26
annotation_background_separation	0.1
branch_bracket_width	0.5
branch_bracket_depth	0.75
c1	clade_marker_color	#FF0000
c1	clade_marker_size	35
c1	class_label	Genomes containing gene X
c11	clade_marker_color	#00FFFF
c11	clade_marker_size	35
c11	class_label	Genomes containing gene X
c2	clade_marker_color	#0000FF
c2	clade_marker_size	35
c3	clade_marker_color	#00FF00
c3	clade_marker_size	35
#class2	annotation_background_color	#0000FF	
#class2	class_label	Clades in which X is a core gene
clade_marker_size	10	
branch_thickness	0.5
Bacill.Bacillale	class	c3
Bacill.Bacillale.Staphylococcaceae.Gemella	class	c1
Bacill.Bacillale.Staphylococcaceae	class	c1
Bacill.Bacillale.Staphylococcaceae.Jeotgalicoccus	class	c1
Bacill.Bacillale.Staphylococcaceae.Macrococcus	class	c1
Bacill.Bacillale.Staphylococcaceae.Staphylococcus	class	c1
Bacill.Bacillale.Staphylococcaceae.unclassified	class	c1
Bacill.Bacillale.Staphylococcaceae.Macrococcus	class	c1
Bacill.Bacillale.unclassified.AA	class	c1
Bacill.Bacillale.unclassified	class	c1
Bacill.Bacillale.Thermoactinomycetaceae.Planifilum	class	c1
Bacill.Bacillale.Thermoactinomycetaceae.Thermoactinomyces	class	c1
Bacill.Bacillale.Thermoactinomycetaceae.unclassified	class	c1
Bacill.Bacillale.Thermoactinomycetaceae	class	c1
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	class	c11
Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	class	c11
Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	class	c11
Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	class	c11
Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	class	c11
Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	class	c11
Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	class	c11
Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	class	c11
Clostridi.Clostridiale.Veillonellaceae.Selenomonas	class	c11
Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	class	c11
#Bacill.Bacillale.Staphylococcaceae	class	class2
#Bacill.Bacillale.Thermoactinomycetaceae	class	class2
#Bacill.Bacillale	class	class2
Bacill.Bacillale	annotation	Y
Bacill.Bacillale.Staphylococcaceae	annotation	Y1
Bacill.Bacillale.Thermoactinomycetaceae	annotation	Y2	
Bacill.Bacillale.unclassified	annotation	Y3
Bacilli.Lactobacillales.Aerococcaceae	class	c2
Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	class	c2
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	class	c2
Bacilli.Lactobacillales.Aerococcaceae.unclassified	class	c2
Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	class	c2

Bacill.Bacillale.Staphylococcaceae.Gemella	ring_shape	1	v
Bacill.Bacillale.Staphylococcaceae.Jeotgalicoccus	ring_shape	1	v
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_shape	1	v
Bacill.Bacillale.Staphylococcaceae.Staphylococcus	ring_shape	1	v
Bacill.Bacillale.Staphylococcaceae.unclassified	ring_shape	1	v
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_shape	1	v
Bacill.Bacillale.unclassified.AA	ring_shape	1	v
Bacill.Bacillale.Thermoactinomycetaceae.Planifilum	ring_shape	1	v
Bacill.Bacillale.Thermoactinomycetaceae.Thermoactinomyces	ring_shape	1	v
Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_shape	1	v
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_shape	1	v
Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_shape	1	v
Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_shape	1	v
Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_shape	1	v
Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_shape	1	v
Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_shape	1	v
Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_shape	1	v
Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_shape	1	v
Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	ring_shape	1	v
Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	ring_shape	1	v
Clostridi.Clostridiale.Veillonellaceae.Selenomonas	ring_shape	1	v
Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	ring_shape	1	v
Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_shape	1	v	
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_shape	1	v
Bacilli.Lactobacillales.Aerococcaceae.unclassified	ring_shape	1	v
Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	ring_shape	1	v

Bacill.Bacillale.Staphylococcaceae.Gemella	ring_width	1	0.6
Bacill.Bacillale.Staphylococcaceae.Jeotgalicoccus	ring_width	1	0.6
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_width	1	0.6
Bacill.Bacillale.Staphylococcaceae.Staphylococcus	ring_width	1	0.6
Bacill.Bacillale.Staphylococcaceae.unclassified	ring_width	1	0.6
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_width	1	0.6
Bacill.Bacillale.unclassified.AA	ring_width	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.Planifilum	ring_width	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.Thermoactinomyces	ring_width	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_width	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_width	1	0.6
Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_width	1	0.6
Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_width	1	0.6
Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_width	1	0.6
Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_width	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_width	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_width	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_width	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	ring_width	1	0.6
Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	ring_width	1	0.6
Clostridi.Clostridiale.Veillonellaceae.Selenomonas	ring_width	1	0.6
Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	ring_width	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_width	1	0.6	
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_width	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.unclassified	ring_width	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	ring_width	1	0.6

Bacill.Bacillale.Staphylococcaceae.Gemella	ring_height	1	0.6
Bacill.Bacillale.Staphylococcaceae.Jeotgalicoccus	ring_height	1	0.6
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_height	1	0.6
Bacill.Bacillale.Staphylococcaceae.Staphylococcus	ring_height	1	0.6
Bacill.Bacillale.Staphylococcaceae.unclassified	ring_height	1	0.6
Bacill.Bacillale.Staphylococcaceae.Macrococcus	ring_height	1	0.6
Bacill.Bacillale.unclassified.AA	ring_height	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.Planifilum	ring_height	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.Thermoactinomyces	ring_height	1	0.6
Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_height	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_height	1	0.6
Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_height	1	0.6
Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_height	1	0.6
Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_height	1	0.6
Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_height	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_height	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_height	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_height	1	0.6
Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	ring_height	1	0.6
Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	ring_height	1	0.6
Clostridi.Clostridiale.Veillonellaceae.Selenomonas	ring_height	1	0.6
Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	ring_height	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_height	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_height	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.unclassified	ring_height	1	0.6
Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	ring_height	1	0.6
