help

("an

nota

tion"

)200 nt

feat1 feat2 feat3

help

("an

nota

tion"

)200 nt

feat1 region1

help

("an

nota

tion"

)200 nt

feat1feat2

feat3

feat1feat2

feat3

feat1Bfeat1C

feat1D

help

("an

nota

tion"

)20 kb

BB

BG

BH

BQ

folCaddBlysK

1.42 Mb1.43 Mb1.44 Mb

dnaJrdgB

ubiB

1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb

addBaccD

10 kb 20 kb 30 kb 40 kb

ubiE hrcA

50 kb 60 kb 70 kb 80 kb

argBcmk

90 kb 100 kb 110 kb 120 kb

trxA

20 kb 30 kb

argBnthpheT

yfeD

90 kb 100 kb 110 kb 120 kb

hrcAargB

80 kb 90 kb

ihfBptsNprfC folC ubiE ptsH

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ap

ply_

colo

r_sc

hem

e")

200 nt

help

("ar

tem

isC

olor

s")

1.0 1.2 1.4 1.6 1.8 2.0

05

1015

rep(1, nrow(artCol))

artC

ol$n

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

white

dark grey

red

green

blue

cyan

magenta

yellow

pale green

light sky blue

orange

brown

pale pink

light grey

black

mid red

light red

pink

help

("au

to_a

nnot

ate"

)10 nt

− atpCatpB

atpAatp2

− − cda1cda2

cda3vcx23

vcx22vcx21

cde20− gfrU gfrT gfrY gfrX gfrW

atpC−A atp2 cda1−3 vcx23−21 cde20 gfrU−T gfrY−W

Eco00

01

atpC

−A

atp2 Eco

0006

Eco00

07

cda1

−3

vcx2

3−21

cde2

0

Eco00

15

gfrU

−T

gfrY

−W

1 atpC−A atp2 6 7 cda1−3 vcx23−21 cde20 15 gfrU−T gfrY−W

help

("ba

rto"

)500 kb

BB

BG

BH

BQ

help

("ch

rY_s

ubse

g")

20 kb 40 kb 60 kb 80 kb 100 kb 120 kb 140 kb 160 kb 180 kb 200 kb

0 kb 20 kb 40 kb 60 kb 80 kb 100 kb 120 kb 140 kb 160 kb 180 kb 200 kb

help

("ge

ne_t

ypes

")2 kb

help

("ge

ne_t

ypes

")2 kb

arro

wshe

adles

s_ar

rows

block

s

bars

point

s

text

lines sid

e_blo

cks

side_

bars

side_

point

s

side_

text

side_

lines

intro

ns

exon

ssid

e_ex

ons

polA BH00110

arro

wshe

adles

s_ar

rows

block

s

bars

point

s

text

lines sid

e_blo

cks

side_

bars

side_

point

s

side_

text

side_

lines

intro

ns

exon

ssid

e_ex

ons

polA BH00110

help

("ge

ne_t

ypes

")200 nt

*** *** ***

***

help

("ge

noP

lotR

−pa

ckag

e")

200 nt

help

("m

auve

_bbo

ne")

500 kb

B_bacilliformis

B_grahamii

B_henselae

B_quintana

help

("pl

ot_g

ene_

map

")200 nt

help

("pl

ot_g

ene_

map

")200 nt

help

("pl

ot_g

ene_

map

")200 nt

A aaa

B bbb

C ccc

help

("pl

ot_g

ene_

map

")200 nt

A aaa

B bbb

C ccc

help

("pl

ot_g

ene_

map

")200 nt

97

78

A aaa

B bbb

C ccc

help

("pl

ot_g

ene_

map

")200 nt

97

78

A aaa

B bbb

C ccc

help

("pl

ot_g

ene_

map

")200 nt

A aaa

B bbb

C ccc

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

feat1 feat2 feat3

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

feat1 region1

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

0 nt 200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

2 kb2.2 kb2.4 kb2.6 kb2.8 kb3 kb3.2 kb3.4 kb3.6 kb

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

0 nt 200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

2 kb 2.2 kb 2.4 kb 2.6 kb 2.8 kb

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")

Comparison of A, B and C

200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")

Comparison of A, B and C

200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")200 nt

Huey

Dewey

Louie

help

("pl

ot_g

ene_

map

")200 nt

Huey

Dewey

Louie

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")200 nt

A_aaa

B_bbb

C_ccc

help

("pl

ot_g

ene_

map

")10 kb

BB

BG

BH

BQ

1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb 1.42 Mb 1.43 Mb 1.44 Mb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb 90 kb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("pl

ot_g

ene_

map

")

BB

BG

BH

BQ

1.42 Mb1.44 Mb 1.38 Mb 1.4 Mb

20 kb 40 kb 60 kb 80 kb

help

("pl

ot_g

ene_

map

")10 kb

BB

BG

BH

BQ

1.42 Mb1.43 Mb1.44 Mb 1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb 90 kb 100 kb 110 kb 120 kb

20 kb 30 kb 90 kb 100 kb 110 kb 120 kb 80 kb 90 kb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("pl

ot_g

ene_

map

")10 kb

BB

BG

BH

BQ

1.42 Mb1.43 Mb1.44 Mb 1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb 90 kb 100 kb 110 kb 120 kb

20 kb 30 kb 90 kb 100 kb 110 kb 120 kb 80 kb 90 kb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("pl

ot_g

ene_

map

")10 kb

BB

BG

BH

BQ

1.42 Mb1.43 Mb1.44 Mb 1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb 90 kb 100 kb 110 kb 120 kb

20 kb 30 kb 90 kb 100 kb 110 kb 120 kb 80 kb 90 kb

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("pl

ot_g

ene_

map

")

geno R

Plot

help

("re

ad_f

unct

ions

")500 kb

B_bacilliformis

B_grahamii

B_henselae

B_quintana

help

("re

ad_f

unct

ions

")500 kb

B_bacilliformis

B_grahamii

B_henselae

B_quintana

help

("re

ad_f

unct

ions

")500 kb

B bacilliformis

B quintana

B henselae

B grahamii

help

("re

ad_f

unct

ions

")5 kb

BH

BQ

help

("re

vers

e")

500 kb

B_bacilliformis

B_grahamii

B_henselae

B_quintana

help

("re

vers

e")

500 kb

B_bacilliformis

B_grahamii

B_henselae

B_quintana

help

("se

g_pl

ot")

●

●

●

●●

●

●

●

●

●

● ●

●

●

help

("se

g_pl

ot")

help

("se

g_pl

ot")

200 nt

1234

0 nt 200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

2

4

6

200 nt 400 nt 600 nt 800 nt 1000 nt 1200 nt

5

6

7

2 kb 2.2 kb 2.4 kb 2.6 kb 2.8 kb 3 kb 3.2 kb 3.4 kb 3.6 kb

help

("se

g_pl

ot")

Random plots for the same segment in 4 Bartonella genomes

20 kb

BB

BG

BH

BQ

250

300

350

1.42 Mb1.43 Mb1.44 Mb 1.38 Mb 1.39 Mb 1.4 Mb 1.41 Mb

100

150

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb 90 kb 100 kb 110 kb 120 kb

50

100

150

20 kb 30 kb 90 kb 100 kb 110 kb 120 kb 80 kb 90 kb

50

100

150

10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 70 kb 80 kb

help

("th

ree_

gene

s")

200 nt

help

("tr

im")

5 kb

BB

BG

BH

BQ