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1、f.nyAlignment Windows Help匝1 遮a pub ZeAlignment Expl o rer/CLU ST AL Op&ni Saved Alignment Sessio-nDo- BLAST Searcti Query Databanks Show Web BrowserVi&w/Edit Sequencer FilmsL Open a saved alignmentL Retrieve sequences I击Alignment Exporer/CLUSTAL”Select ar Option:Create new aiignmenli打开MEGA 软件点击“Ali
2、gnment 一:rM4: Alignment Editor .点击“OKJ点击“Edit”再点击“Insert Sequence From File”弹出对话框后选择所要选择的碱基序列（.tx格式）M4: ClustalW ParametersDNAPar wise ParametersGap Opening PenaltyGap Extension PenallyUse Negative Matrix|dff =“OK”Delay Divergent Cutoff K 厂 Keep Predefined Gcps? Help| y okjX CarcelPairwise alignment
3、Multiple alignment该程序自动完成以后点击图中；P.瓯矣A1磬栏:|间刷 脂went玳:.IIIIII IIIIM 械4： AligramEn? ExplorerData Edit eardn AJignmc-nt We-b tquenctr DispJy HripAlcallgeneaAlcBLigcesBp皿砧,3-H.Q3171S3Alcbligne-s faecaliar0&5-394Alcaligcjic-H零死9Alc&ligne-a raeEaliaSq3737-9nJLlcallgenee faecal i&a43aB51 aAlcbllgvzi3 reEali
4、iHg2171?2AlcaLlgenea 玲JUcBllgEnes 5E：-CgS9333nI啊li X：.计ten 至皎女哄的“Data”选项再点击“Export-ir -l=* .； xir r .1. ：Alignment 选项中的“ MEGA Format”一.123回宕存为伴存在.T.atM i.i i窒可日仆：俱叶算机EYQ文件缶 CHJ :|123l ra取消再点击“保存”f回 kUc /lErminfc Ejq血e0 吼F & Si. * -l抽森蛛#| y由乂 iP X n电雷引*DMA|TTniiiiiiiiiiiiiiiiii_凹项TTT:!S:2:322232;3iBZ
5、35333:S3Z3Z2:32Ei33:3ZS:3ZZlQSUUputa tErtiMU欢村咨E19!H3E3?9!Q!1?E9 IM用骂!9939033313130391!就日HMlLgK CHiMlisfTMSlSiLuIluu EMCil.aJ7&7blU.041L|933Z3ZE123ZEZEEZ3Z3SEEEi!3B!3：3!0：3：3：3!3：33!Q3399QE993Ea3EEI98E33EI93噩噩器匪S3 我:的2非H3 33339B93ESB3i3ORBBIE !333333B!SS 33!S33!333S舞臼 ?9：3 !3SEMCilsGflJfiaaLMmILdm印
6、EMMllBTIKLTLSa!S323!93H39：iaSB：3SB!O3!&309119!9!999931993B393O!9!IS 39133333S3里罚;型咨噩 33!S3SJ933333!3 崩HMlLgit，fbeiHlLM；敏TL9WIkLulLgau xp.DIZllDUMUputa，P，BE站怕LmIluu xp.HQ3LTi.l3!胞*1瞿E站踞哭竟力弭】 ；Q金里金噩;EE矗噩胡3 3B3939339RE19B3EQ9393939339393333133 竟里噩H3 E9RQIB3QES 业噩】驻非5题;焉Sl3Eb Eiii*|*川期 w曲 Eequencer。坏哧 H
7、e/点击Yes出现出现Fil& Data Ditanc&c PhyiogEfiy Patse-yn &lediDn Alignment Windows Help幽提厨叫也 ctia cllb 睫 31EG.%CM峻蜡据Ji加占fileCiting IdZGA in pM硕 &Go 血您6%展f*钮f出现界面在工具栏中点击Phylogeny”f 选择Construct Phylogeny”f 选择Neighbor-Joining (NJ)fCompute”回 IM4: Tree Explorer (C:User5SYQDesktop123.nn-egJI 1=1 I 回File Image Su
8、btree View Compute Ciaptioni HelpA-2Alcaligenes sp.H-Q3171Alcaligenes faecalisGQ4G8851Alcaligenes faecalisAY823619Alcaligenes faecalisFJ959394-Alcaligenes sp.HQ2S2549Alcaligenes faecalisGQAlcaligenes faecalisHQ：Alcaligenes faecalisGO376709Alcaliaenes faecalisHQ317194一再点SBL = 165.82282768File Data Di
9、stances Phylogeny Patt&m Selection Alignment VJindows Help击图中的“Phylogeny” f选择“Bootstrap Test of phylogeny ” f 点击 “ Neighbor-Joining ” f 出现= |回Options SummaryIrclude ites： Test of Phlogeriy OptionSelectionDatd TpeNucleotide Coding),.ri.dlysisPhyloq eny reccinstru ctinnTree Inference- MethodNeighbor-J
10、oining-PhylLiqeny T est and uptiunsBootstrap 1 000 replicates; seed=E423SI nclude Sites-Gdps/Missing DataComplete Deletion-Cudon Posit ions1 sk2nd+2rd-i-N oncodingSutistitutior Model-? ModelNucleotide: Maximum Composite LikelihaodSubstitutions to Included: T ransitions + T ransversionsnTCompute X Ca
11、ncel)? Help1回 MW: Analysis Preferences点击Compute”r回 M4: Tree Explorer (C:UsersSVQDes lctop123.meg)File Image Subtree View Compute Caption Help昌瓯飘咨苣年嗜年Original tree Bootstrap consensus tree62A-228Alealigenes sp.HQ3171Alcaligenes faecalisGQ438351Alcaligenes faecalisAY823619A leal igenes faecal isF J 95
12、9-3 94-Alcaligenes sp.HQ26254995 Alcaligenes fa&calisGQ Alcaligenes faecal is HQ；22I Alcaligenes faecalisGQ376789 二|SBL= 165.02282768成系统发育树的构建如图:faecalisGQ3757B9Alcaligenes faecalisHQ317194 Alcaligenes sp.00993330M4s Tree Explorer CsxUsersVSVQSDesktopXlSSegFile Trnage Subtree View Compute Caption Help炬W9C轮&商一雄废Al勇lig如篮 sp_HQ317193 Alcaligenes faecaliGQ438361Alcaligenes fa0cali&Y823619Alcaligenes faecalisFJ959394AJcaligenes sp_HQ262649AJcaligenes faecalisGQ37579D fa ecal isHQ317192还可以点击对话框中的“ Bootstrap consensus tree ”， 转化图形如下：瓯 M4: Tre e Explorer C:User5SVQDesktcipL2.J
