进化树(Phylogenetic_tree)

1、用PHYLIP构葩化树冯伟，北医三曉血管医学研黑所sno oppyyy二 Aiisers7733mgDto«VJto®R-p9OD-hz-CMrclhe=暫AAJReolbGI ssieiiiuim-u-oottDAXa-LleLlcosstQm ffnvnvjrs53fiI5V09S09W oon®«o«ns C22 Qu rO a4a E o 3 y-G® 的 gpodsk&cuwKJm <J5E1Q3-3O3-uMfi-007p33J Moffitt ofuaiauI mnoonnycdsJ#83v>o-ow

2、 33 ffic32HunK mrtbsffl5INQOCaJhkm 曲ullblc 5;p S Q i N 一 iom ylokjaiOJB4a s L OCRaa EmLa.ascomycetesI o w- - wT ID-off!301- wsQFrLal FC mlfGD - O3C wlj-sshlqq smcffs. jO ron 也 2lcm r I o 叶 r®toowwwo & CR5chytrids basidiomycetes进化树(Phylogenetic tree)分析对于一个完整的进化树分析需要以下几个步骤n To align sequences

3、,要对所分析的多序列目标进行排列；常用的软件有：CLUSTALX 和 CLUSTALW。To reconstrut phyligenetic tree,构建一个进化树;3对进化树进行评估。主要釆用Bootstraping法。当前的任务是:2使虾列序州使用PHILIP软件包中轆離和獣简约法分析进化树口 !484501Mo3ATCTAITTCGTACAmCTOCAGCCACCATCMTAWACGGTACCAT.!.Mol2ATOTAmCTACAmCTOCAGCCACCATCAATATTOTACGGTACCAT.!.Mo9ATGTATCTCGTACATTACTGCCAGCCACCATGAATATTG

4、TACGGTACCATJMol3ATGTATCTCGTACAmCTGCCAGCCACCATGAATATTGTACGGTACCAT.!.Mo6ATOTATTTCGTACAmCTGCCAGCCACCATGMTATTCTACGGTACCAT.!Mo7ATOTATTTCGTACAmCTGCCAGCCACCATGAATATTGTACAGTACCAT.!Mo8ATCTAWGTACAmCTGCCAGCCACCATCAATATTGTACAGTACCAT.!Mo5ATGTATTTCGTACmACTGCCRGCCACCATGMTAnUT曲 GGTACCAT卜第一种方法：最大简约法首先用ClustalW比对序列。使

5、用SEQBOOT产生重复随机序列。使用DNAPARS构造进化树。首先用CLUSTALX对齐序列，输出l.phy,文本编辑器打开后如下图：Mo3501ATCTATTTCGTACATTACTGCCAGCCACCATCAATATTGCNo5ATOTATTTCGTACAITACTOCCAGCCACCATCAATATTOTMo6ATCTATTTCGTACATTACTGCCAGCCACCATCAATATTCTMo7Mo81 ATGTATTTCGATGTATTTCGTACATTACTGTACATTACTCNo9ATGTATCTCGTACATTACTCMol3ATCTATCTCGTACATTACTCMol2A

6、TCTATTTCGTACATTACTGCCAGCCACCATGAATATTCTCCAGCCACCATGAATATTGTCCAGCCACCATGAATATTOTCCAGCCACCATCAATATTCTCCAGCCACCATCAATATTCTACGGTACCAT 4-ACGGTACCAT dACGGTACCAT 】ACAGTACCAT IACAGTACCAT 4-ACGGTACCAT I ACGGTACCAT J. ACGGTACCAT 4-550字节'10行口Text行lr列1简体中文GB2312)共8个序列，每个序列50个碱基。EE然后，打开软件SEQBOOT,如下图巳电子课件（研一2

7、004年第一学期物信息方法与工具softwarephylipexe.Randomnumbercan11 f ind input f ile °lnf ile enterE：、电子课件研一）乜004年第一学期、注物信'息方法与工具so£tLipexe忑盂需 t .exe = Please7订E:电子谍件(研一I 2004年第一学期生物信息方法与工具softwarephylipexe. - 口x|(E:、电子课件研一2004年第一学期生物信息方法与工具VsoFtware phylipexeseqboot exe: canJ t find input file ,pinf

8、 ileMPlease enter a new f ile name> 1-phyRan don number seed, (must be odd>?rbBootstrapping algorithm, uersion 36Settings for this run:DSequence,. Morph, Rest., Gene Freqs?Moleculap sequencesJBootstrap, Jackkn ife. or Permute?BootstrapBBlock size for block-bootwtrapping?1 Cpegular bootstapRHow

9、 nany replica100WRead weights of characNoGRead catec(ories of sites?NoFWrite out data sets or just we ight£?Data setsIInput sequences interleaued?Ves0Terminal type <IBM PC, ANSI, none>?ANSI1Print out the data at start of runNo2Print indications of progress of runVesVto accept these or t i

10、/pe the letteu forone to changed1=Bootstraping法就是从整个序列的碱基（氨基酸）中 任意选取一半，剩下的一半序列随机补齐组成一个 新的序列。这样，一个序列就可以变成了许多序列。 一个多序列组也就可以变成许多个多序列组。根据 某种算法（最大简约性法、最大可能性法、除权配对法或邻位相连法）每个多序列组都可以生成一个 进化树。将生成的许多进化树进行比较，按照多数 规则（majorityrule）我们就会得到一个最“逼真” 的进化树。R选项让使用者输入republicate的数目。所谓 republicate就是用Bootstrap法生成的一个多序列组。8M

11、o 13504-AATGTATTTGTATTAACCCCCAAACCCCAATAATTTGGGTTAACTCTTTT4AATGTATTTGTATTAACCCCCAAACCCCAATAATTTGGGTTAACTCTTTTMo 3AATGTATTTGTATTAACCCCCAAACCCCAATAATTTCGGCCxCTCTTTT4-Mo 5AATGTATTTGTATTAACCCCCAAACCCCAATAATTTGGGTTAACTCETMo8AATGTATTTGTATTAACCCCCAAACCCCAATAATITGGGTTAACTCTTITMo9AATGTATTTCTATTAACCCCCAAACCCC

12、AATAATTTGGGTTAACTCTTTTMo 12AATGTATTTGTATTAACCCCCAAACCCCAATAATTTGGGTTAACTCTTTT4网850 卜AATGTATTTCTATTAACCCCCAAACCCCAATAATTTCGGTTAACTCTTTT4-Mo 12TTGmTCAAAAATMAACTTTGACATGGGATATGGGTAACCGGGTCCAT1Mo 7TTGTTTTCAAAAATAAAACTTTGACATGGGATATGGGTCCGGGTCCxTMo 5TTCTTTTCAAAAATAAAACTTTCACATGGGATATCGGTAACCGGGTCCxT4-Mo9

13、TTCTCTTCAAAAATAAAACTTTGACATCGGATATCGGTAACCGGGTCCxT4-Mo 3TTGmTCAA.AAATMAACTTTGACATGGGATATGGGCAACCGGGTCCATMo8TTGTTTTCAAAAATAAAACTTTGACATGGGATATGGGTAACCGGGTCCATMo 13TTGTCTTCAAAAATAAAACTTTGACATGGGATATGGGTAxQtCCGGGTCCAT4Mo6850TTCTTTTCAAAAATAAAACTTTGACATCGGATATGGGTAACCGGGTCCxT4-Mo 3ATGTTTCGAAATTCCTOCCAAGC

14、CCAT.UATAATITITOGGGTAACCCTT1Mo9ATGTCTGGAAATTCCTGCCAAGCCCATJixAATAATmTGGGGTAACCCTTMo 12ATVTTTCGAAATTCCTGCCAAGCCC也 TAAATAATHTTGGGGTAACCCTT47打开输出文件，如图，得到了 100组序列集。文件为2,out57z300 字节上 901 行.Text行匕列1简体中文(GB2312)打开 DNAPARS2 E:电子课件（研一）2004年第一学期性物信息方法与工具softwarephylipexe.*E：电子課件（研1）年第一学期生物信息方法与工具5FtiwiFephyl

15、ipexednaipaF±s.exe： can1t find input file HinfileHPlease enter a new file nane> 2out输入Seqboot的输出文件，2,outE：电子棵件研i） 2004年第一学期生物信息方注与Zsoftwarephylipexednapar s.exe： the filHoutfile" that you wanted touse as output file already existsDo you want to Replace it# Append to it#writo a new File

16、or Quit?（please type R, F, or Q> 新建dnapars的输出文件3,out2# E:电子课件（研一I 2004年第一学期生物信息方祛与工具softwarephylipexe.enter a new £ile name> 3,0111Nfi parsinony alg-orithn, version M6Ettinc( for this run :2# E:电子课件（研一I 2004年第一学期生物信息方祛与工具softwarephylipexe.Search far best tree?Ves2# E:电子课件（研一I 2004年第一学期生物信

17、息方祛与工具softwarephylipexe.Search opt ion? Number of trees to save? Randomize input order af sequences?Outgroup root? Use ThreshoId parsimony? Use TFansuers ion parsimony? Sites weighted? finalize multiple data set右？ Input sequences interleaved? Terninal type (IBM PC, ANSI, none>? Print out the detE

18、 at start af runMore tliorough search100No. Use in put orderHo, use as Qiitgroup species 1No, use ordinary parsimonyNo. count all stepsNoNoVesANSINo2# E:电子课件（研一I 2004年第一学期生物信息方祛与工具softwarephylipexe.2 Print indie視tions of progress a£ run Ves3 Print out tree Ves4 Print out steps in each site No5

19、Print sequences a/t all nodes of tree NoWriout trees onto tree £ ile? Ves2# E:电子课件（研一I 2004年第一学期生物信息方祛与工具softwarephylipexe.2# E:电子课件（研一I 2004年第一学期生物信息方祛与工具softwarephylipexe.to accept these or typelett" forone to changeaccept these or type the letter for one to change m 修敌参数MMultiple data s

20、ets or multiple weights? (type D or W) dHou many data sets?100Random numbei1 seed (nust be odd)?umber of times to jumble?确定运行后就会出现下面这个dnapars.exe - S用程序错误入Px0040d6封指令引用的UxOOOOOSSf内存口该内存不能为Bread要终止程序请单击"确定；要调试程序诵单击嘲霁PHYLIPPHYLIP is 劝住 package of programs for infemng phylogenies. It is distribute

21、d as source code, documentation files, and a number of different types of executables. These Web pages, by JoeFel型讹in of the Department of Genome Sciences and the DepaTtoienf of Biology at the Uni饰ityof'V和lingon. contain information on PHYLIP and ways to transfer the executables, source code and

22、 documentation to your computer.New as of 2 December 2004:PHYLIP 3.63 is now available. For details on getting PHYLIP see the link below HGet Me PHYLr.采用变通的办法，下载新版Dnapars ver3. 61DNfl parsivnony algorithn.Setting For this Urun:Search for best tree? Search option? Number of trees to saue? Randomize i

23、nput order of sequences?Outgroup root? Use ThreshoId parsinony? Use Transuersion parsinony? Sites weighted? Analyze nultiple data sets? Input sequences interleaved? Terminal tipe <IBM PC, ANSI, none>? Print out the data at start of run Print indications of progress of runPrint out tree Print o

24、u/t steps in eacFi site Print sequences all nodes of tree Write out trees onto tree file?VesMore thorough search 10000No. UseNo. u.se No, useinput order as outgroup species ordinary parsinonvNo. count all stepsNo NoYesIBM PCNoYes VesNo NoVesV to accept these or type the letter Far one to changeV to

25、accept nMultiple data dHow nany dataRandom number seed Cnust be odd>?o change or W>同样修改参数Mthese or type tlw Wtter for one sets or multiple werhts? Itype DNumber of times to junble? 50成功运行!dnaparsl.exe： thE file Uoutti*eeu that you uanted to use as output tree file already exists. Do you uant t

26、o Replace it, Append to it, writ巳 to a neu Filej. or Quit?(please type R, A. F, or Q>Please enteF a neu f ile name> dnaparsj.olittpee最后Dnapars ver3.61 输出二个文件，分别命名为dnapars,outfile和dnapars，outtree最后运行consense，导入dnapaxs, outtreeE：屯(亦1丿004平昂土初衍思力低勺丄貝soft问期讪呱加乜)乜0朋切 se.exe： canJt find input tree fi

27、le "intpeeHPlease enter a neu file nane> dnaparsouttpeeE：电子谏件闌£创04年第-学期姓物宿息方袪与工具5卄阪补卩11卩300耐11 se.exe： the file "outfile" that you wanted touse as output file already existsDo you want to Replace it. Append to it,write to a new File or Quit?(please type R, A, F, op Q)fPlease e

28、nter a new file name consense.ontfile2JHHajority-pule and strict consensus tree progpan, uersion 3.6ettings for this run:0(hitcjroup Foot：No, use as outgroup species 1RTrees to be treated as Rooted：NoTTerminal type (IBM PC, ANSI, none)：ANSI1Print out the sets of species：Ves2Print indications of prog

29、ress of run：¥es3Print out tree：Ves4Write out trees onto tree file：Vesfire these settings correct? (type Y or the letter for one to change)打开 consense, out fileCONSENSUS TREE : -1tine nuunb ears-ttie oirk s indLi c aX e "ttie nuEnrib ezrr-1o±" -t ±iTi.es -ttie g：ir ouLp c ott

30、ls ± s：-t ±n.g: odf "ttie sp e： c± e s-1- wtii dr autre! ± o 七匕©5 xr igki± odE- ±lns.± dE ozrrk o c ci inrjrr e dL-J ajnxoxig ±lne ±r eeotjl± o±" 1OO. OO ees 4-第二种方法，邻位相连法首先执行SEQBOOT软件将这8个序列变成100 个republicate ；DNADIST软件，把SEQBOOT生成

31、的文件输A； 执行NEIGHBOR,输入DNADIST的输出文件;CONSENSE,查看最后结果。运行DNADIST,导入Seqboot的输出文件K F:电子课件（研一）200件第一学期生物信息方注与工具softwarephylipexe. 冋X E：电子课件（研）P004年第一学期生物信息方法与工具巳phylipexEdnadi$3 t.exe: can't £ind input file Hinfile11Please enter a new file name2oiitE：电子课件（研_） 004年第一学期生物信息方法与工具XsoFtnai*巳phylipexednad

32、is t.exe： the file MoutfileH that you wanted touse as out put file alreadii exists.Do you uant to Replace it. Append to it,writE to a new File, or Quit?（please type R. A> F, or Q>fPlease enter a neu file name> dnadlstoutfile并且命名DNADIST的生成丈件为dnadi比outfileY to accept these op type the letter

33、for one to change AIransition/transuersion rat io?16V to accept these or type the letter for one to change 沁磺嚥.皿心如D or ” Hou nan9 data sets?100修改参数T,键入1530之间的数字；修改参数M,改为100运行后生成文件如下图Kol30-00000-00000.04140-00000. 00000-00000.00000.0000J.Mo 70.00000 00000.04140 0000# 00000. 04140.00000.0000o.oooo.;Mo

34、 30.04140.04140.00000.04140.04140.04140.0414Mo 50.00000.00000.04140.00000. 00000.00000.00000.0000.Mo80.00000 00000.04140 00000. 00000.00000.00000.0000.JrMo90.00000.00000.04140.00000. 00000.00000.00000.0000；Mol20.00000.00000.04140.00000. 00000.00000.00000.0000Mo68 JrMol20.00000 00000.04140 00000. 000

35、00.00000.00000.0000J.0.00000.00000.00000.02040.02040.00000.02040.0000Mo 70.00000 00000.00000.02040.02040.00000.02040.0000.Mo 50.00000 00000.00000.02040. 02040.00000.02040.0000.xMo90.02040.02040.02040.00000.04120.02040.00000.0204.1Mo 30.02040.02040.02040.04120. 00000.02040.04120.02044,Mo80.00000 0000

36、0.00000.02040. 02040.00000.02040.0000J.Mol30.02040.02040.02040 00000. 04120.02040.00000.0204.；Mo6SjrMo 30.00000.00000.00000.02040. 02040.00000.02040.0000/0.0000002030.00000 00000. 00000.00000.02030.0000.JrMo90.02030.00000.02030.02030. 02030.02030.00000.0203；Mol20.00000.02030.00000.00000. 00000.00000

37、.02030.0000J.Mo 50.0000002030.00000 00000.00000.00000-02030.0000161f500 字节 j901 行口Text行1,列1简体中文CGB2312)这个文件包含了与输入文件相同的100个 republicate,只不过每个republicate是以两 两序列的进化距离来表示。文件中的每个 republicate都省略了第一排的Mo3 Mo5 Mo6Mo7 Mo8 Mo9 Mo12 Mo13o以这个输出文件为输入文件，执行NEIGHBOR软件k E:电子iS件（研1） 2004年第一学期'生物信息方徳与工具softwarephyl

38、ipexe. - XE：电子懐件册1) 2郦年第-学期曲躺息方站工具softwuephylipexeneighh士or.exe： can't find input file "infile11Please entei1 a neu file nane> dnadist,outfileE：軒謀件(朋j) 2004年第-学期姓物宿息方法与工具softimFep)ylipe5«neighb or.exe： the file youtfileH that you wanted touse as output file already existsDo you want

39、 to Replace i Append to 毎 write to a new File, or Quit?(please type R, ft, F, or Q)FPlease enter a new file nane> neighbor,outfileNe ighbor-Jo in in g/U PGMfi method version 3.6 £ettings for this pun:ighbor-Joining or UPGMfi thee? Oiitgroup root?Neighbor-joiningNo, use as outgroup speciesLow

40、er-trianulap data matrix? NoUpper-trianulai1 data matrix?Subreplicates?Randomize input order of species?NoNoNo. Use input orderMAnalyze multiple data sets? No0 Terminal type <IBM PC, ANSI. none>? ANSI1Print out th巳 data at start of run No2 Print indications of progress of run ¥es3 Print o

41、ut tree ¥es4 Write out trees onto tree file? VesV to accept these or type the lettei? for one to change修改M的参数为100ighbor-Joining/UPGMAhod version 3.6etting$ for this run:N0M012Neighbor-joiningNo use as outgroup speciesNoNoNoNo. Use in put order¥es, 100 setsNoVesVesVesNe ighhor-jo in ing or UPGNA tree? Outgroup root? Lower-triangular data matrix? Upper-triangular data natrix? Subreplicat巳台？ Randomize input order of species? Analyze multiple data sets?Term