如何利用iTOL绘制漂亮的进化树

建树,利用iTOL美化自己的树

看了网站诸多文章,感觉还是有很多的不明便,索性,我自己写一个教程(不全哦)。

通常呢,我们要经历一下步骤:

1、序列比对

我们应用clustalw进行比对,clustalw下载连接(http://www.clustal.org/download/current/

选择自己需要的版本

attachments-2019-04-8pKhjsHw5ca5770d6952e.jpg

clustalw-->test.fa-->2-->1-->test.dnd-->test.aln-->X#clustalw调用该函数#test.fa输入比对数据#2选择多序列比对#1进行比对#选择输出文件*.dnd#选择输出文件*.aln#退出X

或者可以直接用MEGA7.0或者MEGA-X直接进行比对

1.1序列

attachments-2019-04-SfT8pG2t5ca5703aad12e.jpg

1.1 序列

以7条序列为例,保存为test.fa

>WWW000001
MAADGFFATLTRCRNNHFWFTVFALFVLWYLLLYVHDWSFRISNVDTAAAATATEFIHSTENPSYFLDEPITFTHPEKIGQNPIDLIPTDEIPVPEKELK
PPALVRQRSLPNFEPPVKQRLRRNTTVENRRIKREPKRSCKNRYIYVHDLPTRFNLDFLEDCLSLSQWSDMCRYLTNSGMGPFLGNPQNLFSDTGWFITN
QFSLEVIFHNRMKQYECLTNDSSKAAAVFVPYYAGLDVARFLWGGFNTSVRDADAIGMAKWLTEKPEWKTMYGKDHFFIAGRITWDFRRGIDDDDAWGNK
LMLLPEVKNMTVLTIESSPWNENDFGIPYPTYFHPSDDGEIVNWQAKMRKIKRKTLFSFAGAPRAHLEGSIRGEVIAQCAASKRRCKLLQCGDNNLNKCY
KPFHVMKMFQGSVFCLQPPGDSYTRRSTFDSILAGCIPVFFTPGSAYVQYLWHLPRDFFKYSILIPEDDVKGKRVSIERVLSRVSRARITAMREEVIKLI
PKVVYADPRSRRLEAVEDAFDLAVKGVLERVERERRRENVSDGEFFDEEYSWKYHLFGNFEKHEWDHYFARS
>WWW000002
MGRRRPSIHDIQTVSPAFTISHISSPTNTENSFSGFSPINYHGMMAPIYGGNFADESLFLAPITATMAVANAGRDQPSAAFYPSYLPLSSPMNRNWG
>WWW000003
MKSPFEGGRICEEFTPGYYGVCAVGGMLSAGTTHLAITPLDVLKVNMQVHPVKYASIYTCFSSLLKEQGPSAFRRGWTGKFFGYGVQGACRFGLYEYFKK
VYSNVLVDQNKTVVFFISSASAEVIANVALCPFEAIKVKVQAQPHFAKGLTDGFPKLYGSEGIRGLYRGLIPLWGRNLPFSMVMFSSFEHAVDLIYRNVI
RRKKEDCSIPQQLGVTCLAGYAAGSVGSIISNPADNIVASLYNKKAESLKLAVKKIGFVNLFTRSLPIRIMLVGPVVTLQWLFYDTIKLLSGWSTSGNVI
TDTENDGAA
>WWW000004
METPAKSIADVVDEIMGIHRSLPTRPGIDEVEAAKMLIRNIEAEDQSRIEAIARQTKSKDVPEELFRILQEMQKNLVYFQSREQKREAVKLLDLDGVHEL
FDDLIQRASKCLPSSSSASSAYSRSASSRDSSSLSLENTASFSGNSLNSTTATPPVSSSSYIDKAPVKTSELYTRDDSYLKKAKGTLYSDGFRSGNASKP
QIVDSTLKPATTSGQDGEKLSLIKLASLIEASSKKGTKDLILKNKLTDQVEWLPDSIGKLSSLITLDLSENRILLLPSTIGGLSSLTTLDLHSNRLSQLP
ESIGDLLSLVHLDVSANQLTSLPSVIGRLIRLQELKLSSNLLTVLPESIGSLASLQKLDVETNDLEEFPHTIGKCSSLMEIRADYNRLKALPEAVGRISS
LEVLSVRYNNIQQLPTTMASLSSLKELDISFNQLESVPESLCFATTLVKMNISNNFADLQALPRSIGNLEMLEELNMSNNQIRVLPASFRMLSRLRVLNV
EGNPLEVPPRDVVNKGAQAVVQYMADLVENREVKSQPSISVEKLNICSFLLKMNDRYQPEM
>WWW000005
MADTGLNFNEPLNDDGMGGGVLLMKDRKIISRAQYVDSSIKMPPVWNISDLVRKEKIKSVSDMPRLYLCSAPENSHQKREWILFLGYLKEYNKVAIANID
LYELYIFPPHESLKFSHAIVYYCMEKANDVYDSQLHRASEVKSADILSEPPRLVADTSKIDGSAQTTPTSTKSFVHGRVSPLVDFKAVENKLPTDSKFPT
TGSEYAFGSRVEACRGTEPNVMVPSSCLNKNYVRTDPSYLKTLGQAHSGWMFGAIAELVDNSRDAKAAKIQISIDMICSKRAGKEIPMLSVIDDGHGMSH
QEVLRMISFGHKQPDSDDPDRIGRFGIGFKTGAMRLGRDALVLTQTVNSRSIAFLSQSLNEGKDNVEIPIVSYTRTGQIMEVDTSVQSEASAKYNLKAIK
EFSPFNKYLIGEKAGMFHENATGTQIYIWNLEEWGSSFYLEWETGMNGGSSFHQGDIYIRSRRIRSRPGQMSRTVPLDYSLRSYLEVIFLDPRMKIYLQG
SLVRSRPLAKSLNGTVVKNGCILQKPVQLTLGRCQLEREQGNCGIFLYWHGRLIEAYKRVGSMVHNGDKSHGIIGVIDVTDLMDDGKGYAWVHSNKQGFL
DSEAYALLEQWLAEISNEYLDTHVYKILLKKGNGLYKPDHEWVQCDKCRKWRMLNPGFDSKTLPQEWFCYMKPFNGKCEMPEQKIGRGVITVSAKRSGFD
TDKKLREFKDGNDEQTSYTGENSSEDSSGQTVEESTRTSLKRLRRGPPRTCRN
>WWW000006
MEINLGQLPFDIDFHPLDKLVAAGLITGDLLLYRYSADSSPQRLLEVHAHSESCRAVRFINEGHAIVTGSPDCSIIAMDVETGSVIARHENAHGAAVNRI
VNLMQSTIASGDDGGCIKIWDTRQRSCCSSFDAHEEYISDMTFASDSMKLGDGTLSVCNLRSNKIQTRSEFSEDELLSVVIMKNGRKVVCGTQTGNLLLY
SWGFFKDCSDRFVDLSPNSVDALLKLDEDRVITGSENGLISLVGILPNRIIQPIAEHSEYPVERLAFSHDRKFLGSISHDQTLKLWDLDEILEGSGNTVT
ANSTAAGTGSGSGSDSDNDEMDVDTNSLPKSSKASETKGGSKGQEGFNGFFSDL
>WWW000007
MANPGGVGSKYVSANLNKSYGQPPHHNHAPYGGSYGQAASSRTRPGGGGGGMVVLSRNRPLQKAVPKLSIPPPLNLPSLRKEHERFDPSGSTGGGYGGGG
GGGTGGGTRPTSSGMGWTKPVAAIAVEENDGSESRVVNGVDRNMNAFDGISRGSGSYMPPSAKSVTAAPSLAARATVLRGEDFPSLRAALPTTSGPVQKQ
KDNTHKKQKQTVGAESSNLQGEIYQSSLAQIHPRGQSAQRFVGNNGSKESVVGEGFERVGDQTRKQEELFPGPLPMVQLNPRSDWADDERDTGHGFSDRG
RSHELPKNESYWDRDFDIPRSSLPQKPVQNQFNNRWGQHDNNTTSAKEVSGVDPYHRNARTPSNGVGEKASSVDRDLVKENHYTQSHFTNHVIPEARQQL
NHTRDRYSTKQSSRYSSDSFHSNNSASKSSFFPSKSEGIPAKDPKPKFSFSKNEKPYSEDPFLGDERDPFSGGLLGVIKRKKDVVKQPDFHDPVRESFEA
ELERVQQMQEMERRRIVEEHERALEQARREEEERQRLIIEEEQRQRRMEEEAREAAWRVEQERVEAIQRAEELKIAREEEKKKIFMEEERRKQAAKQKLL
ELEAMMAKRQAESKNHVLDVANKKEKDDFKAVDRDEWDDSERMVERIVTSESSGSSFPNRSFEMGSSMSQSFLDRGKHVNMWRKHVFENDNTSSILVQEH
ENGLYSPDRGAYAGGGRAFPRKELYGGAGQMPSRSYYAEERAHLNEHMWSSSGGRDHYGKSRVIEIEPEFHDNLDKRYGDVEWGPSRSHSHHQPPYPGRI
YQHNEGDEIYPYGRSRYSMRQPRVLPPPSLSSMHRTSFRGENEQNKSTFMDDGLIYNHATGNESNMQIEYSDSHQEKLEPSPLLDVHEESAVAGEDEEWP
LENNEDLQGQEEYDEEENGYQEEEEAHEGDDDKIDITQEFEGLHLEDRDSPHMMDNLVLGFNEGVEVGIPSDDFERNQKNEATSNFGVPEVSVVIGDAEG
VPGDGEGLQIGSIQMPLHLHPPVGPSLTHIHPSQPPLFHFGQLRYTSPTSQGLLPVSSHYNLAQNSVPVQPTQETSAQPVVSSSHELPQENILRGLNPLP
VREIMELNVPIHEGGMDISVTGEDKKHQNTDTKVYMPLSKKRGPENQSQNAPASGEKYFSGSNSQGPFPSRGRRFGYSVRNSGMRSEASSYSDSGGFQRM
PRRVIHRTEFRIRENGDRRQSLVDDKSNSDGRGFGRSGSKRSTMSNKPLKLVVEPESSRLDPVSVQETISESRAGKGNGKEAITKSSSTHTIDLKKNDSE
EDVDAPLQSGIVRVFKQSGIEAPSDEDDFIEASLGGEASDIARSEFVVQEGQSVASKEVSTGSMTAVSQPLAPIGTPTVNPSLQDDIRSNTIKSYQTDPV
SVGSSGENDLESGALFESKNKVADDVQTASVSWDSAQINQQVMALTQTQLDEAMKSAQFDAHGATIGGHTNSGSSKPILPSSSILMKDASFSSTASPINS
LLAGEKIQFGAVTSPTVLPPSSRVVTHGVGAPDKHPNEPCVHLEDCEAGAEAAASAVAVAGITCDEIVENGLGPVTVSDVKSSGVVASDQQLGSQFRAEE
SLTVSLPADLSIETPSISLWPPLPSPPNSSTQMPSYFPGGPPPHFPYYEMNPMLGGPIYAFGPHEESSTAQSQAQKSSTAPGSGPLAPWQPCHPVVDSFY
GPPAGFTGPFVGPPGGIPGVQGPPHMVVYNHFAPVGQFGQVGLSFMGTTYIQSGKQPDWKHNPGSGMGMSDGNMDNMNMVSAQRNPANMAAPVQHLAPGS
PLLPMAMFDASPFQPASDISAQAWSRVPASPIHTLPLSQPLQQQQPALHPAQFSRGHPPVDQSLSSTTRFSDPQTSTPQQPPPPPQNNRTFPIVTDPIIT
QFPEELGLVADPATTATTTTNTTNATISQGAAGGSDNCGSHHSKDQNADIFKNRTSQGKIIPPIRQQYGQSMGYNSNYQRGGGGGGVSQKNNMGGNNHRR
VGFQGRNQQSMGVEKGFPPSKMKQVYVPKQTTGS



1.2拖拽test.fa到MEGA-x中

也可以选择粘贴,粘贴的时候选择你比对的序列,此处为蛋白
attachments-2019-04-6ZSnvO6W5ca570ea9da8f.jpg

1.3 比对

比对-->输出*.meg
attachments-2019-04-V1v5AoT45ca5713f87b5c.jpg

1.4将输出的.meg文件拖拽会MEGA-X中

选择构建邻近(NJ)系统发育树
bootstrap选择1000

attachments-2019-04-Er57svoK5ca571966f078.jpg

1.5保存为*.nwk格式

attachments-2019-04-3I9gh4ez5ca572069d7f7.jpg

2、进入iTOL1.0版本的官网

其实也有其他的2个工具可以进行绘制如:
Figtreehttp://tree.bio.ed.ac.uk/software/figtree/

2.1注册

attachments-2019-04-sBecOFsI5ca572f293ffc.jpg

2.2提交序列

选择左下角的上传树文件
attachments-2019-04-9E31agsl5ca5731ee2eab.jpg点击进入主页面
attachments-2019-04-rbp5XIba5ca5733f7ed5d.jpg

2.3添加颜色,转变类型

attachments-2019-04-MVALgjCB5ca573728b067.jpg
基础设置attachments-2019-04-y6Wb8pUv5ca5744436e80.jpg
给树添加颜色和背景色
attachments-2019-04-X3wVBfW75ca575076cdce.jpg为ID添加形状
attachments-2019-04-dVqNYVGG5ca57616830c0.jpgattachments-2019-04-rvj8zOZS5ca5765bade86.jpg
放上几张官网的美图
First slide


TOL
unroot.png

好勒,至此大致讲完,具体的细节,得看你的需要,记得别忘了引用哦
如果有侵犯您版权或疑惑,请电邮:smyang2018@gmail.com

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