# Darwin script to draw distance trees of
#    69 Archaea
# Downloaded from http://www.biorecipes.com/Orthologues/status.html
# (C) 2010 CBRG, ETH Zurich

tree := Tree(Tree(Tree(Tree(Tree(Leaf(Color(MidnightBlue,NANEQ),-46.9110,13),
-5.2775,Tree(Tree(Leaf(Color(red,NITMS),-52.5012,54),-38.2974,Leaf(Color(red,
CENSY),-53.5761,37),100),-5.5985,Tree(Leaf(Color(DarkGreen,KORCO),-48.8694,51),
-9.2503,Tree(Leaf(Color(red,THEPD),-45.0668,35),-11.3368,Tree(Tree(Tree(Leaf(
Color(red,IGNH4),-43.8521,45),-18.3289,Tree(Tree(Leaf(Color(red,STAMF),-43.6441,
39),-28.4977,Leaf(Color(red,DESK1),-48.2490,56),100),-19.2611,Tree(Leaf(Color(
red,HYPBU),-41.2421,36),-21.4299,Leaf(Color(red,AERPE),-46.4417,6),100),91),100)
,-16.2684,Tree(Leaf(Color(red,METS5),-48.2062,49),-31.1053,Tree(Tree(Leaf(Color(
red,SULAC),-48.1980,22),-35.4413,Leaf(Color(red,SULTO),-45.5693,18),100),
-32.0533,Tree(Leaf(Color(red,SULSO),-47.3545,4),-46.5796,Tree(Tree(Tree(Leaf(
Color(red,SULIK),-47.6647,67),-47.6188,Tree(Leaf(Color(red,SULIM),-47.6887,61),
-47.6361,Leaf(Color(red,SULIA),-47.7114,58),99),100),-47.5062,Tree(Leaf(Color(
red,SULIN),-47.6358,62),-47.5205,Leaf(Color(red,SULIY),-47.5619,59),42),88),
-47.4277,Leaf(Color(red,SULIL),-47.4277,60),100),100),100),100),100),-13.1060,
Tree(Leaf(Color(red,CALMQ),-50.2168,46),-24.5739,Tree(Leaf(Color(red,PYRCJ),
-50.2512,33),-43.1727,Tree(Tree(Leaf(Color(red,THENV),-50.5621,52),-45.8004,Leaf
(Color(red,PYRIL),-50.3817,32),100),-43.2819,Tree(Leaf(Color(red,PYRAR),-49.9683
,38),-44.0797,Leaf(Color(red,PYRAE),-49.4753,3),100),57),100),100),94),100),100)
,57),100),-1.5698,Tree(Leaf(Color(purple,THESM),-32.3969,68),-22.1222,Tree(Tree(
Leaf(Color(purple,THEON),-30.9327,23),-26.5610,Tree(Leaf(Color(purple,THEGJ),
-30.8903,65),-27.5126,Leaf(Color(purple,PYRKO),-30.7303,21),100),100),-22.6689,
Tree(Leaf(Color(purple,PYRFU),-31.3527,17),-27.8321,Tree(Leaf(Color(purple,PYRAB
),-31.1637,16),-29.0328,Leaf(Color(purple,PYRHO),-31.5024,11),100),100),65),100)
,87),-0.9560,Leaf(Color(red4,METKA),-32.8291,10),72),-0.2959,Tree(Tree(Tree(Leaf
(Color(orange,METTH),-33.5335,9),-16.5838,Tree(Leaf(Color(orange,METS3),-37.7028
,41),-17.8304,Leaf(Color(orange,METST),-37.6918,26),97),100),-4.9138,Tree(Tree(
Leaf(Color(MediumBlue,META3),-38.1910,43),-23.8286,Tree(Leaf(Color(MediumBlue,
METVS),-38.4942,44),-32.1013,Tree(Leaf(Color(MediumBlue,METMP),-38.5130,15),
-36.7662,Tree(Tree(Leaf(Color(MediumBlue,METM6),-38.4482,53),-37.6794,Leaf(Color
(MediumBlue,METM7),-38.4874,42),100),-37.2489,Leaf(Color(MediumBlue,METM5),
-38.4944,47),100),100),100),100),-17.8159,Tree(Leaf(Color(MediumBlue,METVM),
-33.9253,69),-29.9220,Tree(Leaf(Color(MediumBlue,METFA),-33.0426,66),-30.7614,
Leaf(Color(MediumBlue,METJA),-32.8030,1),100),100),100),100),-2.4019,Tree(Leaf(
Color(IndianRed,ARCFU),-32.7850,7),-5.5750,Tree(Tree(Tree(Tree(Leaf(Color(cyan,
NATPD),-47.3786,24),-35.5231,Tree(Tree(Leaf(Color(cyan,HALMD),-47.7483,63),
-39.8581,Leaf(Color(cyan,HALMA),-47.7692,20),100),-37.1020,Leaf(Color(cyan,HALUD
),-47.8589,64),100),100),-34.1512,Tree(Leaf(Color(cyan,HALS3),-49.7127,50),
-49.7127,Leaf(Color(cyan,HALSA),-49.7659,8),100),92),-33.7164,Tree(Leaf(Color(
cyan,HALWD),-48.7861,27),-35.3250,Leaf(Color(cyan,HALLT),-48.0952,57),91),100),
-9.2480,Tree(Tree(Tree(Leaf(Color(green,METHJ),-42.3797,28),-24.5037,Tree(Leaf(
Color(green,METMJ),-40.4920,40),-25.5906,Tree(Leaf(Color(green,METPE),-42.2452,
55),-27.8916,Leaf(Color(green,METB6),-41.7708,48),100),100),100),-23.3126,Leaf(
Color(green,METLZ),-44.0490,34),100),-12.1968,Tree(Leaf(Color(LightSeaGreen,
UNCMA),-38.4591,30),-13.7661,Tree(Leaf(Color(green,METTP),-38.0130,31),-14.1530,
Tree(Leaf(Color(green,METBU),-38.9394,29),-22.9518,Tree(Leaf(Color(green,METBF),
-38.5676,25),-34.4040,Tree(Leaf(Color(green,METAC),-38.4026,5),-35.7648,Leaf(
Color(green,METMA),-38.3496,2),100),100),100),63),100),100),100),100),100),100),
0,Tree(Leaf(Color(black,PICTO),-44.1818,19),-22.7452,Tree(Leaf(Color(black,THEAC
),-41.5543,14),-35.0060,Leaf(Color(black,THEVO),-41.4875,12),100),100)) :
title := 'All Archaeal genomes (max Length)  (only 1 isoform used) , Sat Jan 30 14:33:04 2010, 69 species, 19681 orthologs, 18 top groups, 199 used here, Weighted, BestSubset, DimlessQual: best: 1.6454, ave: 1.752 +- 0.012, var: 0.04041, Z=-0.5293':
Xref := [LTEXT(110,3,'Crenarchaeota',color = [1, 0, 0]), LTEXT(110,6,'Methanomicrobia',color = [0, 1, 0]), LTEXT(110,9,'Methanococci',color = [0, 0, 0.8039]), LTEXT(110,12,'Halobacteria',color = [0, 1, 1]), LTEXT(110,15,'Thermococci',color = [0.6275, 0.1255, 0.9412]), LTEXT(110,18,'Methanobacteria',color = [1, 0.6471, 0]), LTEXT(110,21,'Thermoplasmata',color = [0, 0, 0]), LTEXT(110,24,'Archaeoglobi',color = [0.8039, 0.3608, 0.3608]), LTEXT(110,27,'Methanopyri',color = [0.5451, 0, 0]), LTEXT(110,30,'environmental samples',color = [0.1255, 0.6980, 0.6667]), LTEXT(110,33,'Korarchaeota',color = [0, 0.3922, 0]), LTEXT(110,36,'Nanoarchaeota',color = [0.09803922, 0.09803922, 0.4392])]:

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