# Darwin script to draw distance trees of
#    224 Gammaproteobacteria
# Downloaded from http://www.biorecipes.com/Orthologues/status.html
# (C) 2011 CBRG, ETH Zurich

tree := Tree(Tree(Tree(Tree(Leaf(Color(red4,LEGLN),-37.8532,224),-27.9660,Tree(
Leaf(Color(red4,LEGPC),-38.3205,107),-37.9530,Tree(Tree(Leaf(Color(red4,LEGPL),
-38.5510,27),-38.0698,Leaf(Color(red4,LEGPH),-38.4404,26),86),-38.0121,Leaf(
Color(red4,LEGPA),-38.4131,25),57),100),100),-6.7111,Tree(Leaf(Color(red4,COXB2)
,-36.8705,184),-36.8661,Tree(Leaf(Color(red4,COXBN),-37.1663,147),-36.9965,Tree(
Leaf(Color(red4,COXBR),-37.1819,148),-37.0945,Leaf(Color(red4,COXBU),-37.1418,18
),100),88),100),41),-4.1462,Tree(Tree(Tree(Leaf(Color(SpringGreen,DICNV),
-48.6824,100),-7.0003,Tree(Tree(Tree(Tree(Leaf(Color(purple,STRM5),-43.1745,165)
,-41.8156,Leaf(Color(purple,STRMK),-42.9049,132),100),-33.6211,Tree(Tree(Tree(
Leaf(Color(purple,XANC5),-43.3956,62),-42.6225,Leaf(Color(purple,XANAC),-43.2763
,33),100),-41.8833,Tree(Leaf(Color(purple,XANOR),-43.4230,30),-43.4230,Tree(Leaf
(Color(purple,XANOM),-43.5933,68),-43.4950,Leaf(Color(purple,XANOP),-43.5659,159
),84),100),100),-40.5968,Tree(Leaf(Color(purple,XANCB),-43.2543,131),-43.0830,
Tree(Leaf(Color(purple,XANC8),-43.2134,45),-43.1896,Leaf(Color(purple,XANCP),
-43.2505,3),98),100),100),100),-31.9389,Tree(Leaf(Color(purple,XYLFA),-44.3905,
28),-43.7656,Tree(Leaf(Color(purple,XYLFM),-44.7021,153),-44.2661,Tree(Leaf(
Color(purple,XYLF2),-44.9070,152),-44.8793,Leaf(Color(purple,XYLFT),-44.9066,2),
100),100),100),100),-7.8968,Tree(Tree(Tree(Tree(Leaf(Color(LightSeaGreen,ALHEH),
-36.1355,103),-17.4038,Leaf(Color(LightSeaGreen,HALHL),-39.4811,79),100),
-10.5141,Leaf(Color(LightSeaGreen,THISH),-33.9681,196),95),-9.4119,Tree(Leaf(
Color(LightSeaGreen,NITOC),-36.5418,53),-9.6792,Leaf(Color(grey30,METCA),
-35.5336,36),43),64),-8.2861,Tree(Leaf(Color(MidnightBlue,ACIF2),-47.3450,185),
-47.2792,Leaf(Color(MidnightBlue,ACIF5),-47.2792,179),100),35),90),84),-5.2479,
Tree(Tree(Tree(Leaf(Color(DarkGreen,MARMS),-37.3447,127),-9.1984,Tree(Leaf(Color
(DarkGreen,ALCBS),-36.9722,66),-9.3784,Tree(Tree(Leaf(Color(gold,CELJU),-34.4798
,163),-15.4681,Tree(Leaf(Color(green,SACD2),-36.8409,69),-20.3439,Leaf(Color(
green,TERTT),-36.3672,203),100),99),-10.0226,Tree(Leaf(Color(DarkGreen,CHRSD),
-36.7424,58),-10.6414,Tree(Tree(Leaf(Color(grey50,AZOVD),-33.6770,220),-24.1667,
Tree(Tree(Leaf(Color(MediumBlue,PSEU5),-33.4752,87),-24.7787,Tree(Leaf(Color(
MediumBlue,PSEA7),-33.1405,125),-32.3888,Tree(Leaf(Color(MediumBlue,PSEA8),
-32.9872,188),-32.9463,Tree(Leaf(Color(MediumBlue,PSEAB),-33.1027,88),-32.9870,
Leaf(Color(MediumBlue,PSEAE),-33.0824,6),60),100),100),47),-24.6161,Tree(Leaf(
Color(MediumBlue,PSEMY),-33.0689,113),-25.1455,Tree(Tree(Leaf(Color(MediumBlue,
PSEE4),-34.1367,89),-31.7403,Tree(Tree(Leaf(Color(MediumBlue,PSEPG),-34.2191,126
),-33.3584,Tree(Leaf(Color(MediumBlue,PSEP1),-34.1079,115),-33.8488,Leaf(Color(
MediumBlue,PSEPK),-33.9956,40),100),100),-32.4320,Leaf(Color(MediumBlue,PSEPW),
-34.2743,130),100),100),-27.5725,Tree(Tree(Leaf(Color(MediumBlue,PSEFS),-34.6788
,200),-30.8682,Tree(Leaf(Color(MediumBlue,PSEPF),-34.3245,59),-31.1183,Leaf(
Color(MediumBlue,PSEF5),-34.0722,50),93),100),-29.2421,Tree(Tree(Leaf(Color(
MediumBlue,PSEU2),-34.6219,51),-33.7989,Leaf(Color(MediumBlue,PSE14),-34.6000,49
),100),-33.4933,Leaf(Color(MediumBlue,PSESM),-34.7196,15),100),100),100),75),91)
,100),-10.7341,Tree(Leaf(Color(green,MARAV),-35.3270,77),-14.3694,Leaf(Color(
DarkGreen,HAHCH),-35.2539,60),100),69),100),99),73),99),-7.5720,Tree(Tree(Leaf(
Color(IndianRed,ACIAD),-41.8702,35),-35.9535,Tree(Tree(Tree(Leaf(Color(IndianRed
,ACIB3),-41.4204,181),-41.3981,Tree(Leaf(Color(IndianRed,ACIB5),-41.4441,182),
-41.4117,Leaf(Color(IndianRed,ACIBY),-41.4532,142),61),93),-41.2717,Tree(Leaf(
Color(IndianRed,ACIBC),-41.4340,141),-41.3281,Leaf(Color(IndianRed,ACIBS),
-41.6468,162),78),81),-41.0297,Leaf(Color(IndianRed,ACIBT),-41.0297,91),100),100
),-19.4390,Tree(Leaf(Color(IndianRed,PSYWF),-42.5212,114),-32.3737,Tree(Leaf(
Color(IndianRed,PSYCK),-44.4403,56),-42.7322,Leaf(Color(IndianRed,PSYA2),
-44.4900,149),100),100),100),88),-6.6781,Tree(Tree(Tree(Tree(Leaf(Color(green,
PSEA6),-37.8807,73),-22.6117,Leaf(Color(green,ALTMD),-38.0352,161),100),-15.8434
,Tree(Leaf(Color(green,PSEHT),-38.8303,54),-16.9780,Leaf(Color(green,COLP3),
-38.6183,46),100),83),-13.7458,Tree(Tree(Leaf(Color(green,PSYIN),-40.5939,97),
-15.1192,Tree(Tree(Tree(Tree(Tree(Tree(Leaf(Color(red,BLOFL),-60.0818,29),
-39.4113,Leaf(Color(red,BLOPB),-55.6929,48),100),-30.5314,Tree(Leaf(Color(red,
WIGBR),-70.1137,23),-34.6426,Tree(Leaf(Color(red,BUCBP),-71.8220,43),-41.2229,
Tree(Leaf(Color(red,BUCCC),-85.3946,81),-42.3266,Tree(Tree(Leaf(Color(red,BUCAT)
,-66.3683,191),-66.3528,Tree(Leaf(Color(red,BUCA5),-66.6274,197),-66.5062,Leaf(
Color(red,BUCAI),-66.6491,19),96),100),-51.6183,Leaf(Color(red,BUCAP),-68.2801,
14),100),49),99),98),98),-21.4718,Tree(Leaf(Color(red,HAMD5),-44.8770,206),
-24.1725,Tree(Leaf(Color(magenta2,BAUCH),-50.5710,76),-24.2205,Tree(Leaf(Color(
red,PROMH),-38.5444,167),-26.1658,Tree(Tree(Leaf(Color(red,PHOAA),-38.1397,205),
-35.3368,Leaf(Color(red,PHOLL),-38.0799,24),100),-27.3842,Tree(Leaf(Color(red,
EDWI9),-38.0783,210),-27.6512,Tree(Tree(Tree(Tree(Leaf(Color(red,SERP5),-36.4381
,124),-31.1877,Tree(Leaf(Color(red,YERE8),-37.0582,83),-34.9114,Tree(Tree(Tree(
Leaf(Color(red,YERP3),-37.2488,134),-37.2101,Tree(Tree(Tree(Leaf(Color(red,YERPD
),-37.3278,213),-37.3170,Tree(Leaf(Color(red,YERPA),-37.3498,67),-37.3298,Tree(
Leaf(Color(red,YERPE),-37.3557,22),-37.3372,Tree(Tree(Leaf(Color(red,YERP1),
-37.3837,217),-37.3541,Leaf(Color(red,YERPG),-37.4008,160),50),-37.3432,Leaf(
Color(red,YERPN),-37.3595,78),22),24),38),51),-37.3024,Leaf(Color(red,YERPP),
-37.3140,95),94),-37.2240,Leaf(Color(red,YERPY),-37.2539,155),86),78),-37.1912,
Leaf(Color(red,YERPS),-37.2070,34),77),-37.1639,Leaf(Color(red,YERPB),-37.1639,
154),100),100),100),-29.3621,Tree(Tree(Leaf(Color(red,DICDC),-37.7753,214),
-32.9564,Leaf(Color(red,DICZE),-37.5232,209),100),-30.9632,Tree(Leaf(Color(red,
PECCP),-36.9519,207),-35.8194,Leaf(Color(red,ERWCT),-37.3735,13),100),100),100),
-28.4642,Tree(Leaf(Color(red,ERWT9),-38.0825,164),-29.3967,Tree(Leaf(Color(red,
ENTS8),-37.1518,139),-32.5156,Tree(Tree(Leaf(Color(red,KLEP7),-37.3164,121),
-36.9369,Leaf(Color(red,KLEP3),-37.4378,173),100),-33.5329,Tree(Leaf(Color(red,
ENT38),-37.8522,116),-33.5973,Tree(Tree(Tree(Leaf(Color(red,CITK8),-37.1618,146)
,-35.1699,Tree(Leaf(Color(red,SALAR),-37.6820,122),-36.8324,Tree(Tree(Tree(Leaf(
Color(red,SALPK),-37.4564,166),-37.4371,Leaf(Color(red,SALPA),-37.4708,32),100),
-37.3006,Tree(Leaf(Color(red,SALA4),-37.4189,177),-37.3123,Tree(Tree(Tree(Tree(
Tree(Leaf(Color(red,SALPB),-37.4446,150),-37.3408,Tree(Leaf(Color(red,SALDC),
-37.4656,174),-37.3845,Tree(Leaf(Color(red,SALG2),-37.5020,178),-37.4017,Leaf(
Color(red,SALEP),-37.4393,172),100),100),80),-37.3320,Tree(Leaf(Color(red,SALHS)
,-37.4232,169),-37.3390,Leaf(Color(red,SALTY),-37.4161,44),65),59),-37.3294,Leaf
(Color(red,SALNS),-37.4050,168),94),-37.3208,Tree(Leaf(Color(red,SALPC),-37.4451
,202),-37.3994,Leaf(Color(red,SALCH),-37.4753,31),100),67),-37.3145,Leaf(Color(
red,SALSV),-37.4431,171),47),72),69),-37.2756,Leaf(Color(red,SALTI),-37.4598,8),
100),100),100),-35.0477,Leaf(Color(red,CITRI),-37.4451,222),100),-34.8648,Tree(
Tree(Tree(Leaf(Color(red,ECO7I),-37.3000,189),-37.1806,Leaf(Color(red,ECOSM),
-37.2868,137),99),-37.1591,Tree(Leaf(Color(red,ECO27),-37.3511,199),-37.2336,
Tree(Leaf(Color(red,ECOL6),-37.3234,10),-37.2439,Tree(Tree(Tree(Leaf(Color(red,
ECO45),-37.3417,195),-37.3042,Tree(Leaf(Color(red,ECOK1),-37.3438,101),-37.3079,
Leaf(Color(red,ECOUT),-37.3397,74),76),100),-37.2602,Leaf(Color(red,ECO81),
-37.3577,194),94),-37.2493,Leaf(Color(red,ECOL5),-37.3437,63),73),94),100),89),
-37.1454,Tree(Tree(Tree(Tree(Leaf(Color(red,ECO5T),-37.3164,208),-37.2917,Leaf(
Color(red,ECO5E),-37.3165,175),100),-37.2826,Leaf(Color(red,ECO57),-37.3095,17),
100),-37.1783,Tree(Leaf(Color(red,SHIDS),-37.4656,61),-37.1794,Tree(Tree(Tree(
Tree(Leaf(Color(red,ECO24),-37.3107,123),-37.2363,Tree(Tree(Leaf(Color(red,ECO55
),-37.3019,190),-37.2396,Leaf(Color(red,ECO8A),-37.3048,201),32),-37.2379,Tree(
Leaf(Color(red,ECOSE),-37.3083,180),-37.2413,Leaf(Color(red,ECO10),-37.3168,218)
,44),46),99),-37.2176,Tree(Tree(Leaf(Color(red,ECOLC),-37.3089,136),-37.2454,
Tree(Tree(Leaf(Color(red,ECOBD),-37.3154,221),-37.2865,Leaf(Color(red,ECOBB),
-37.3146,204),100),-37.2495,Tree(Leaf(Color(red,ECOBW),-37.3199,212),-37.2991,
Tree(Leaf(Color(red,ECOLI),-37.3203,1),-37.3019,Tree(Leaf(Color(red,ECODH),
-37.3446,133),-37.3083,Leaf(Color(red,ECOD1),-37.3254,223),60),52),100),68),89),
-37.2340,Leaf(Color(red,ECOHS),-37.2896,135),100),62),-37.2124,Tree(Leaf(Color(
red,SHIF8),-37.4678,92),-37.3904,Leaf(Color(red,SHIFL),-37.4877,21),100),38),
-37.2113,Tree(Leaf(Color(red,SHISS),-37.3616,52),-37.2298,Tree(Leaf(Color(red,
SHIB3),-37.4116,158),-37.3143,Leaf(Color(red,SHIBS),-37.4013,55),100),94),100),
38),87),-37.1673,Leaf(Color(red,ECOLU),-37.2757,186),89),100),100),93),100),100)
,100),98),-27.9511,Leaf(Color(red,SODGM),-38.5514,57),100),100),100),100),56),
100),98),-19.8319,Tree(Tree(Tree(Leaf(Color(cyan,HAEDU),-45.0225,47),-36.8670,
Tree(Leaf(Color(cyan,ACTP7),-43.5524,156),-43.3487,Tree(Leaf(Color(cyan,ACTPJ),
-43.7126,143),-43.4271,Leaf(Color(cyan,ACTP2),-43.7345,105),84),100),100),
-34.9086,Leaf(Color(cyan,HAEPS),-42.9095,192),100),-29.2268,Tree(Tree(Tree(Leaf(
Color(cyan,HAES2),-43.0448,144),-42.6868,Leaf(Color(cyan,HAES1),-42.9833,75),100
),-32.4819,Tree(Tree(Tree(Leaf(Color(cyan,AGGAN),-42.3550,219),-38.8751,Leaf(
Color(cyan,AGGAD),-42.6617,215),100),-33.8087,Tree(Tree(Leaf(Color(cyan,HAEIN),
-42.6044,4),-42.1865,Tree(Leaf(Color(cyan,HAEIE),-43.3966,104),-42.4801,Leaf(
Color(cyan,HAEI8),-42.7307,38),94),95),-41.7942,Leaf(Color(cyan,HAEIG),-41.8363,
102),100),100),-32.8819,Leaf(Color(cyan,PASMU),-41.3622,5),100),80),-32.2626,
Tree(Leaf(Color(cyan,ACTSZ),-43.0067,129),-33.8642,Leaf(Color(cyan,MANSM),
-41.9689,39),100),100),100),98),-18.0813,Tree(Leaf(Color(orange,PHOPR),-37.4125,
9),-24.4864,Tree(Tree(Leaf(Color(orange,ALISL),-38.1912,176),-34.1227,Tree(Leaf(
Color(orange,VIBFM),-37.5603,170),-37.1095,Leaf(Color(orange,VIBF1),-37.2860,37)
,100),100),-26.5486,Tree(Tree(Leaf(Color(orange,VIBC3),-37.1564,145),-37.0956,
Tree(Leaf(Color(orange,VIBCM),-37.1675,198),-37.1648,Tree(Leaf(Color(orange,
VIBCJ),-37.2063,211),-37.2063,Leaf(Color(orange,VIBCH),-37.2805,11),100),100),
100),-29.5867,Tree(Leaf(Color(orange,VIBSL),-38.2017,193),-30.4962,Tree(Tree(
Leaf(Color(orange,VIBHB),-37.2237,151),-34.7305,Leaf(Color(orange,VIBPA),
-36.9460,16),100),-31.6790,Tree(Leaf(Color(orange,VIBVU),-37.0386,20),-36.8558,
Leaf(Color(orange,VIBVY),-37.0134,7),100),100),100),100),100),100),98),-16.5330,
Tree(Leaf(Color(brown,AERS4),-35.4436,84),-33.2637,Leaf(Color(brown,AERHH),
-35.1249,80),100),98),94),-14.7175,Tree(Leaf(Color(green,SHEAM),-36.4378,109),
-27.0680,Tree(Tree(Tree(Leaf(Color(green,SHEFN),-38.1607,71),-30.1066,Leaf(Color
(green,SHEDO),-37.9101,64),100),-28.8870,Tree(Tree(Tree(Leaf(Color(green,SHEPC),
-36.8790,112),-36.7500,Leaf(Color(green,SHESW),-36.8738,93),100),-34.6353,Tree(
Leaf(Color(green,SHEB9),-37.0861,117),-36.8745,Tree(Leaf(Color(green,SHEB5),
-37.0848,110),-36.8793,Tree(Leaf(Color(green,SHEB2),-37.0818,183),-36.8956,Leaf(
Color(green,SHEB8),-37.0880,111),69),37),100),100),-33.6152,Tree(Tree(Leaf(Color
(green,SHESA),-36.7605,85),-36.2630,Tree(Leaf(Color(green,SHESM),-36.6931,99),
-36.4986,Leaf(Color(green,SHESR),-36.7730,65),100),100),-35.2982,Leaf(Color(
green,SHEON),-36.7640,12),100),100),100),-27.8116,Tree(Tree(Tree(Leaf(Color(
green,SHESH),-38.1920,119),-33.4642,Leaf(Color(green,SHEWM),-38.2515,140),100),
-30.5759,Tree(Tree(Leaf(Color(green,SHEHH),-38.0466,128),-35.8273,Leaf(Color(
green,SHEPA),-37.9118,118),100),-33.6525,Leaf(Color(green,SHEPW),-38.2378,187),
100),100),-29.8747,Leaf(Color(green,SHELP),-37.3580,82),100),100),100),90),83),
-12.8858,Leaf(Color(green,IDILO),-38.2213,42),98),92),56),-4.7401,Tree(Tree(Leaf
(Color(HotPink,RUTMC),-44.2886,106),-36.9551,Leaf(Color(HotPink,VESOH),-46.1976,
94),100),-8.1739,Leaf(Color(purple4,THICR),-38.7388,70),73),32),100),0,Tree(Leaf
(Color(black,FRAP2),-40.1430,138),-34.8508,Tree(Leaf(Color(black,FRATN),-40.2243
,96),-39.6310,Tree(Tree(Tree(Leaf(Color(black,FRATF),-40.1265,120),-40.0788,Leaf
(Color(black,FRATH),-40.1263,90),62),-40.0745,Leaf(Color(black,FRATO),-40.1153,
86),99),-39.8301,Tree(Tree(Leaf(Color(black,FRATW),-40.0973,98),-39.9823,Leaf(
Color(black,FRATM),-40.3026,157),52),-39.9643,Tree(Tree(Leaf(Color(black,FRATT),
-40.1289,41),-40.1018,Leaf(Color(black,FRAT1),-40.1268,72),99),-40.0719,Leaf(
Color(black,FRATE),-40.0719,216),100),93),76),100),100)) :
title := 'All Gammaproteobacteria (max Length)  (only 1 isoform used) , Sun Dec 19 08:41:07 2010, 224 species, 55894 orthologs, 52 top groups, 277 used here, AveVarWeighted, BestSubset, DimlessQual: best: 0.13535, ave: 0.15494 +- 0.00078, var: 0.0001566, Z=-1.566':
Xref := [LTEXT(110,3,'Enterobacteriales',color = [1, 0, 0]), LTEXT(110,6,'Alteromonadales',color = [0, 1, 0]), LTEXT(110,9,'Pseudomonas',color = [0, 0, 0.8039]), LTEXT(110,12,'Pasteurellales',color = [0, 1, 1]), LTEXT(110,15,'Xanthomonadales',color = [0.6275, 0.1255, 0.9412]), LTEXT(110,18,'Vibrionales',color = [1, 0.6471, 0]), LTEXT(110,21,'Francisellaceae',color = [0, 0, 0]), LTEXT(110,24,'Moraxellaceae',color = [0.8039, 0.3608, 0.3608]), LTEXT(110,27,'Legionellales',color = [0.5451, 0, 0]), LTEXT(110,30,'Chromatiales',color = [0.1255, 0.6980, 0.6667]), LTEXT(110,33,'Oceanospirillales',color = [0, 0.3922, 0]), LTEXT(110,36,'Acidithiobacillales',color = [0.09803922, 0.09803922, 0.4392]), LTEXT(110,39,'Aeromonadales',color = [0.6471, 0.1647, 0.1647]), LTEXT(110,42,'sulfur-oxidizing symbionts',color = [1, 0.4118, 0.7059]), LTEXT(110,45,'Piscirickettsiaceae',color = [0.3333, 0.1020, 0.5451]), LTEXT(110,48,'Azotobacter',color = [0.4980, 0.4980, 0.4980]), LTEXT(110,51,'Cellvibrio',color = [1, 0.8431, 0]), LTEXT(110,54,'Baumannia',color = [0.9333, 0, 0.9333]), LTEXT(110,57,'Cardiobacteriales',color = [0, 1, 0.4980]), LTEXT(110,60,'Methylococcales',color = [0.3020, 0.3020, 0.3020])]:

# Uncomment the desired draw command
# or type ?DrawTree for help on the options
DrawTree(tree,ArcRadial,RadialLabels,LengthFormat = '',Title = title,Xref) :
# DrawTree( tree, Phylogram, Legend, LengthFormat='', OrderLeaves=LeftHeavy, Title=title, Xref )):
ViewPlot():