進(jìn)化樹(shù)(Phylogenetic_tree)

1、用PHYLIP構(gòu)葩化樹(shù)馮偉，北醫(yī)三曉血管醫(yī)學(xué)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 葉 r®toowwwo & CR5chytrids basidiomycetes進(jìn)化樹(shù)(Phylogenetic tree)分析對(duì)于一個(gè)完整的進(jìn)化樹(shù)分析需要以下幾個(gè)步驟n To align sequences

3、,要對(duì)所分析的多序列目標(biāo)進(jìn)行排列；常用的軟件有：CLUSTALX 和 CLUSTALW。To reconstrut phyligenetic tree,構(gòu)建一個(gè)進(jìn)化樹(shù);3對(duì)進(jìn)化樹(shù)進(jìn)行評(píng)估。主要釆用Bootstraping法。當(dāng)前的任務(wù)是:2使蝦列序州使用PHILIP軟件包中轆離和獣簡(jiǎn)約法分析進(jìn)化樹(shù)口 !484501Mo3ATCTAITTCGTACAmCTOCAGCCACCATCMTAWACGGTACCAT.!.Mol2ATOTAmCTACAmCTOCAGCCACCATCAATATTOTACGGTACCAT.!.Mo9ATGTATCTCGTACATTACTGCCAGCCACCATGAATATTG

4、TACGGTACCATJMol3ATGTATCTCGTACAmCTGCCAGCCACCATGAATATTGTACGGTACCAT.!.Mo6ATOTATTTCGTACAmCTGCCAGCCACCATGMTATTCTACGGTACCAT.!Mo7ATOTATTTCGTACAmCTGCCAGCCACCATGAATATTGTACAGTACCAT.!Mo8ATCTAWGTACAmCTGCCAGCCACCATCAATATTGTACAGTACCAT.!Mo5ATGTATTTCGTACmACTGCCRGCCACCATGMTAnUT曲 GGTACCAT卜第一種方法：最大簡(jiǎn)約法首先用ClustalW比對(duì)序列。使

5、用SEQBOOT產(chǎn)生重復(fù)隨機(jī)序列。使用DNAPARS構(gòu)造進(jìn)化樹(shù)。首先用CLUSTALX對(duì)齊序列，輸出l.phy,文本編輯器打開(kāi)后如下圖：Mo3501ATCTATTTCGTACATTACTGCCAGCCACCATCAATATTGCNo5ATOTATTTCGTACAITACTOCCAGCCACCATCAATATTOTMo6ATCTATTTCGTACATTACTGCCAGCCACCATCAATATTCTMo7Mo81 ATGTATTTCGATGTATTTCGTACATTACTGTACATTACTCNo9ATGTATCTCGTACATTACTCMol3ATCTATCTCGTACATTACTCMol2A

6、TCTATTTCGTACATTACTGCCAGCCACCATGAATATTCTCCAGCCACCATGAATATTGTCCAGCCACCATGAATATTOTCCAGCCACCATCAATATTCTCCAGCCACCATCAATATTCTACGGTACCAT 4-ACGGTACCAT dACGGTACCAT 】ACAGTACCAT IACAGTACCAT 4-ACGGTACCAT I ACGGTACCAT J. ACGGTACCAT 4-550字節(jié)'10行口Text行l(wèi)r列1簡(jiǎn)體中文GB2312)共8個(gè)序列，每個(gè)序列50個(gè)堿基。EE然后，打開(kāi)軟件SEQBOOT,如下圖巳電子課件（研一2

7、004年第一學(xué)期物信息方法與工具softwarephylipexe.Randomnumbercan11 f ind input f ile °lnf ile enterE：、電子課件研一）乜004年第一學(xué)期、注物信'息方法與工具so£tLipexe忑盂需 t .exe = Please7訂E:電子諜件(研一I 2004年第一學(xué)期生物信息方法與工具softwarephylipexe. - 口x|(E:、電子課件研一2004年第一學(xué)期生物信息方法與工具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法就是從整個(gè)序列的堿基（氨基酸）中 任意選取一半，剩下的一半序列隨機(jī)補(bǔ)齊組成一個(gè) 新的序列。這樣，一個(gè)序列就可以變成了許多序列。 一個(gè)多序列組也就可以變成許多個(gè)多序列組。根據(jù) 某種算法（最大簡(jiǎn)約性法、最大可能性法、除權(quán)配對(duì)法或鄰位相連法）每個(gè)多序列組都可以生成一個(gè) 進(jìn)化樹(shù)。將生成的許多進(jìn)化樹(shù)進(jìn)行比較，按照多數(shù) 規(guī)則（majorityrule）我們就會(huì)得到一個(gè)最“逼真” 的進(jìn)化樹(shù)。R選項(xiàng)讓使用者輸入republicate的數(shù)目。所謂 republicate就是用Bootstrap法生成的一個(gè)多序列組。8M

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

12、AATAATTTGGGTTAACTCTTTTMo 12AATGTATTTGTATTAACCCCCAAACCCCAATAATTTGGGTTAACTCTTTT4網(wǎng)850 卜AATGTATTTCTATTAACCCCCAAACCCCAATAATTTCGGTTAACTCTTTT4-Mo 12TTGmTCAAAAATMAACTTTGACATGGGATATGGGTAACCGGGTCCAT1Mo 7TTGTTTTCAAAAATAAAACTTTGACATGGGATATGGGTCCGGGTCCxTMo 5TTCTTTTCAAAAATAAAACTTTCACATGGGATATCGGTAACCGGGTCCxT4-Mo9

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

14、CCAT.UATAATITITOGGGTAACCCTT1Mo9ATGTCTGGAAATTCCTGCCAAGCCCATJixAATAATmTGGGGTAACCCTTMo 12ATVTTTCGAAATTCCTGCCAAGCCC也 TAAATAATHTTGGGGTAACCCTT47打開(kāi)輸出文件，如圖，得到了 100組序列集。文件為2,out57z300 字節(jié)上 901 行.Text行匕列1簡(jiǎn)體中文(GB2312)打開(kāi) DNAPARS2 E:電子課件（研一）2004年第一學(xué)期性物信息方法與工具softwarephylipexe.*E：電子課件（研1）年第一學(xué)期生物信息方法與工具5FtiwiFephyl

15、ipexednaipaF±s.exe： can1t find input file HinfileHPlease enter a new file nane> 2out輸入Seqboot的輸出文件，2,outE：電子棵件研i） 2004年第一學(xué)期生物信息方注與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的輸出文件3,out2# E:電子課件（研一I 2004年第一學(xué)期生物信息方祛與工具softwarephylipexe.enter a new £ile name> 3,0111Nfi parsinony alg-orithn, version M6Ettinc( for this run :2# E:電子課件（研一I 2004年第一學(xué)期生物信息方祛與工具softwarephylipexe.Search far best tree?Ves2# E:電子課件（研一I 2004年第一學(xué)期生物信

17、息方祛與工具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:電子課件（研一I 2004年第一學(xué)期生物信息方祛與工具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:電子課件（研一I 2004年第一學(xué)期生物信息方祛與工具softwarephylipexe.2# E:電子課件（研一I 2004年第一學(xué)期生物信息方祛與工具softwarephylipexe.to accept these or typelett" forone to changeaccept these or type the letter for one to change m 修敵參數(shù)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?確定運(yùn)行后就會(huì)出現(xiàn)下面這個(gè)dnapars.exe - S用程序錯(cuò)誤入Px0040d6封指令引用的UxOOOOOSSf內(nèi)存口該內(nèi)存不能為Bread要終止程序請(qǐng)單擊"確定；要調(diào)試程序誦單擊嘲霽PHYLIPPHYLIP is 勸住 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型訛in of the Department of Genome Sciences and the DepaTtoienf of Biology at the Uni飾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.采用變通的辦法，下載新版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>同樣修改參數(shù)Mthese or type tlw Wtter for one sets or multiple werhts? Itype DNumber of times to junble? 50成功運(yùn)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 輸出二個(gè)文件，分別命名為dnapars,outfile和dnapars，outtree最后運(yùn)行consense，導(dǎo)入dnapaxs, outtreeE：屯(亦1丿004平昂土初衍思力低勺丄貝soft問(wèn)期訕呱加乜)乜0朋切 se.exe： canJt find input tree fi

27、le "intpeeHPlease enter a neu file nane> dnaparsouttpeeE：電子諫件闌£創(chuàng)04年第-學(xué)期姓物宿息方袪與工具5卄阪補(bǔ)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)打開(kāi) 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-第二種方法，鄰位相連法首先執(zhí)行SEQBOOT軟件將這8個(gè)序列變成100 個(gè)republicate ；DNADIST軟件，把SEQBOOT生成

31、的文件輸A； 執(zhí)行NEIGHBOR,輸入DNADIST的輸出文件;CONSENSE,查看最后結(jié)果。運(yùn)行DNADIST,導(dǎo)入Seqboot的輸出文件K F:電子課件（研一）200件第一學(xué)期生物信息方注與工具softwarephylipexe. 冋X E：電子課件（研）P004年第一學(xué)期生物信息方法與工具巳phylipexEdnadi$3 t.exe: can't £ind input file Hinfile11Please enter a new file name2oiitE：電子課件（研_） 004年第一學(xué)期生物信息方法與工具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的生成丈件為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修改參數(shù)T,鍵入1530之間的數(shù)字；修改參數(shù)M,改為100運(yùn)行后生成文件如下圖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 字節(jié) j901 行口Text行1,列1簡(jiǎn)體中文CGB2312)這個(gè)文件包含了與輸入文件相同的100個(gè) republicate,只不過(guò)每個(gè)republicate是以兩 兩序列的進(jìn)化距離來(lái)表示。文件中的每個(gè) republicate都省略了第一排的Mo3 Mo5 Mo6Mo7 Mo8 Mo9 Mo12 Mo13o以這個(gè)輸出文件為輸入文件，執(zhí)行NEIGHBOR軟件k E:電子iS件（研1） 2004年第一學(xué)期'生物信息方徳與工具softwarephyl

38、ipexe. - XE：電子懐件冊(cè)1) 2酈年第-學(xué)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-學(xué)期姓物宿息方法與工具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的參數(shù)為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巳臺(tái)？ Randomize input order of species? Analyze multiple data sets?Term