生信小技能-推荐两个好用(牛逼)的系统发育树构建工具

小概念

系统发育树：也称为系统进化树或者分子发育树

使用范围

宏基因组，群体基因组等群体进化研究

在线工具

iTol

** Example Tree 文件 **

(((((((((((((((((((155864:0.00000,83334:0.00000)I1:0.00044[96],((217992:0.00000,562:0.00022)I2:0.00022[76],(198215:0.00000,623:0.00000)I3:0.00266[100])I4:0.00000[75])I5:0.00813[100],((209261:0.00000,601:0.00000)I6:0.00146[100],602:0.00075)I7:0.00702[100])I8:0.03131[100],((229193:0.00000,(187410:0.00000,632:0.00000)I9:0.00000[31])I10:0.03398[100],141679:0.05076)I11:0.01182[61])I12:0.02183[98],((203907:0.32481,36870:0.35452)I13:0.08332[100],(135842:0.27492,(118099:0.09535,98794:0.10235)I14:0.10140[100])I15:0.06497[100])I16:0.15030[100])I17:0.02808[100],((747:0.03441,727:0.03754)I18:0.01571[94],730:0.05333)I19:0.07365[100])I20:0.03759[100],((((196600:0.00021,672:0.00291)I21:0.01212[100],670:0.01985)I22:0.01536[100],666:0.02995)I23:0.02661[100],74109:0.06131)I24:0.05597[100])I25:0.03492[81],70863:0.10577)I26:0.12234[100],((160488:0.02741,323:0.03162)I27:0.02904[100],287:0.03202)I28:0.14456[100])I29:0.04492[98],((183190:0.01324,2371:0.00802)I30:0.10192[100],(92829:0.01069,340:0.00934)I31:0.05037[100])I32:0.24151[100])I33:0.02475[49],777:0.33185)I34:0.03328[54],((((65699:0.00400,491:0.00134)I35:0.12615[100],536:0.09623)I36:0.07131[100],((520:0.00127,(519:0.00199,518:0.00022)I37:0.00006[67])I38:0.14218[100],305:0.11464)I39:0.08478[100])I40:0.03840[75],915:0.22059)I41:0.08761[100])I42:0.16913[100],((((((181661:0.00000,180835:0.00000)I43:0.05735[100],382:0.05114)I44:0.05575[100],((29461:0.00102,29459:0.00184)I45:0.08660[100],381:0.09308)I46:0.02384[51])I47:0.08637[100],(1076:0.04182,375:0.06346)I48:0.14122[100])I49:0.05767[100],155892:0.23943)I50:0.11257[100],(66077:0.51596,(782:0.04245,781:0.02487)I51:0.38019[100])I52:0.12058[100])I53:0.12365[100])I54:0.06301[100],((((85963:0.00897,210:0.00637)I55:0.19055[100],32025:0.12643)I56:0.05330[100],844:0.11644)I57:0.09105[100],197:0.20399)I58:0.41390[100])I59:0.04428[82],((882:0.38320,(35554:0.22491,959:0.45934)I60:0.04870[43])I61:0.04100[69],(240015:0.24572,234267:0.29086)I62:0.20514[100])I63:0.04214[64])I64:0.05551[98],((76856:0.45615,(63363:0.40986,2336:0.34182)I65:0.07696[100])I66:0.03606[35],(((262724:0.26583,1299:0.29763)I67:0.24776[100],243164:0.53988)I68:0.04370[35],((((103690:0.12014,1148:0.15652)I69:0.04331[98],32046:0.13147)I70:0.05040[100],(((84588:0.06780,74547:0.05434)I71:0.04879[100],1219:0.10211)I72:0.04238[74],59919:0.16170)I73:0.20442[100])I74:0.07646[100],33072:0.23764)I75:0.24501[100])I76:0.04332[39])I77:0.02720[51])I78:0.03471[74],((((214688:0.36751,117:0.38017)I79:0.24062[100],((44275:0.00000,173:0.00027)I80:0.47573[100],((160:0.25544,158:0.16072)I81:0.19057[100],139:0.42323)I82:0.20278[100])I83:0.07248[95])I84:0.04615[42],(((218496:0.00009,203267:0.00081)I85:0.44723[100],216816:0.29283)I86:0.14429[100],(((((196627:0.00022,1718:0.00000)I87:0.03415[100],152794:0.02559)I88:0.03682[100],1717:0.06479)I89:0.13907[100],(((1765:0.00067,(83331:0.00000,83332:0.00000)I90:0.00022[98])I91:0.03027[100],1769:0.05135)I92:0.01514[97],1770:0.02091)I93:0.11523[100])I94:0.09883[100],(33903:0.02680,1902:0.02678)I95:0.16707[100])I96:0.06110[91])I97:0.26800[100])I98:0.03480[23],((59374:0.51984,(1097:0.37204,(837:0.11304,818:0.13145)I99:0.34694[100])I100:0.09237[100])I101:0.04841[62],(((182082:0.00000,(138677:0.00000,(115713:0.00000,115711:0.00000)I102:0.00000[37])I103:0.00000[44])I104:0.10482[100],83557:0.05903)I105:0.04170[98],(83560:0.01938,813:0.02643)I106:0.06809[100])I107:0.60169[100])I108:0.04443[32])I109:0.04284[67])I110:0.02646[66],((119072:0.17512,((1513:0.10918,1502:0.11535)I111:0.03238[78],1488:0.11396)I112:0.15056[100])I113:0.11788[100],(((((267748:0.27702,2107:0.28761)I114:0.28466[100],((((2104:0.10966,2097:0.11268)I115:0.31768[100],2096:0.24373)I116:0.14180[100],28227:0.34890)I117:0.06674[94],134821:0.33874)I118:0.19177[100])I119:0.07341[100],44101:0.37680)I120:0.12541[100],100379:0.47843)I121:0.09099[100],(((((265669:0.00063,1639:0.00144)I122:0.00235[90],1642:0.00248)I123:0.13517[100],((182710:0.13838,86665:0.09280)I124:0.02676[91],(((226900:0.00342,222523:0.00123)I125:0.00573[100],198094:0.00331)I126:0.08924[100],1423:0.07876)I127:0.01984[96])I128:0.03907[100])I129:0.02816[69],((196620:0.00000,(158879:0.00022,158878:0.00022)I130:0.00022[61])I131:0.02479[100],1282:0.03246)I132:0.17366[100])I133:0.02828[64],(((((((216495:0.00110,216466:0.00155)I134:0.01637[100],(1314:0.00134,(186103:0.00045,(198466:0.00000,193567:0.00022)I135:0.00110[100])I136:0.00066[87])I137:0.02250[100])I138:0.01360[100],1309:0.04319)I139:0.01920[99],(171101:0.00119,1313:0.00124)I140:0.03607[100])I141:0.04983[100],1360:0.11214)I142:0.08901[100],1351:0.07946)I143:0.03958[100],(33959:0.20999,1590:0.14371)I144:0.06763[100])I145:0.08989[100])I146:0.08905[100])I147:0.09540[92])I148:0.04315[54])I149:1.34959,(((((296543:0.33483,(237895:0.25048,36329:0.28267)I150:0.14359[100])I151:0.03495[42],(((4530:0.07623,3702:0.09366)I152:0.15770[100],45157:0.38319)I153:0.08133[96],(44689:0.34685,(((33169:0.07298,4932:0.07619)I154:0.21170[100],4896:0.24665)I155:0.15370[100],(((180454:0.10724,7227:0.10233)I156:0.09870[100],((31033:0.03142,7955:0.05230)I157:0.04335[100],(((10116:0.03107,10090:0.01651)I158:0.00398[91],(9606:0.00957,9598:0.03864)I159:0.01549[100])I160:0.01629[99],9031:0.04596)I161:0.01859[100])I162:0.09688[100])I163:0.03693[95],(6239:0.01843,6238:0.01896)I164:0.24324[100])I165:0.09911[100])I166:0.04004[85])I167:0.02708[41])I168:0.02636[44])I169:0.06455[87],5664:0.45664)I170:0.10129[100],184922:0.55482)I171:0.57543[100],((160232:0.81078,(((111955:0.17389,2287:0.18962)I172:0.33720[100],56636:0.43380)I173:0.09462[94],13773:0.55514)I174:0.12018[100])I175:0.15444[100],((50339:0.10412,2303:0.09785)I176:0.66151[100],((((187420:0.36583,2320:0.35331)I177:0.07446[99],(39152:0.28592,2190:0.13226)I178:0.23828[100])I179:0.06284[100],((53953:0.02786,29292:0.02179)I180:0.02239[100],2261:0.02366)I181:0.36220[100])I182:0.04469[51],(2234:0.34660,(64091:0.61597,(2214:0.02602,2209:0.03087)I183:0.30588[100])I184:0.12801[100])I185:0.10395[100])I186:0.06815[62])I187:0.11833[99])I188:0.43325[100])I189:0.88776)100;

# Step 1 Upload Tree file
将 Tree 文件粘贴或者上传至 http://itol.embl.de/upload.cgi 
# Step 2 Set other options
调整基本的图形设置、显示参数及基础发育树的设置
# Step 3 添加注释文件
这个功能可是瞬间使简单的发育树逼格满满，秒上 CNS 封面的节奏
# Step 4 导出图像
默认导出 SVG 矢量格式的图片，使用浏览器打开查看，或者转换为 png 图片格式输出

EvolView

使用 EvolView 之前首先注册一个账户，可以使用 Google 或者 Micoresoft 帐号。
Tree 文件和 iTol 一致，都可以识别多种格式输入数据。

# Step 1 Upload Tree file
将 Tree 文件粘贴或者上传至 http://www.evolgenius.info/evolview/
# Step 2 Set other options
设置不同的分支树风格，还可以导出基础图形
# Step 3 添加注释信息
上传高级选项所需注释文件，可选择不同注释风格
# Step 4 导出结果文件
可以导出多种格式文件

区别：

iTol 是歪果仁搞出来的，可以不需要帐号就可以使用，注释风格需要自己配置文件。

EvolView 是北京基因研究所搞出来的，使用前需要先注册或绑定帐号，不过在使用方面提供了界面式类一键添加功能，可视化程度更高，不需要写复杂的配置文件。

各有优缺点，自行选择使用吧！

参考文献：
1. Ivica Letunic, Peer Bork; Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44 (W1): W242-W245. doi: 10.1093/nar/gkw290

2. He et al, Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees, Nucleic Acids Res, (2016).

3. Zhang et al. EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res (2012) pp. 4.

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