1、MEGA5使用說明MEGA軟件一一系統發育樹構建方法（圖文講解）2012年12月02日/Evolution/字號小史太/評論3條/閱讀3,872次點擊加入在線收藏夾一、莊列文本的準備構樹之前先將目標基因座列都分別保存為txt文本文件中（或者把所有莊列保存在同一個txt文本中，可以用“基因名稱”作為第一行，然后重起一行編輯基因序列）,序列只包含序列字母（ATCG或氨基酸簡寫字母）。文件名名稱可以已經您的想法隨意編輯。1YL 1-1 1 M13F A0( MBMB-1YL_1-1_2JiU3F_E0( WYLJ.-1_3_M13F_C5二YL 1-2 2 M13F E0( £jYL_L-

2、2_3J13F_F0(YL-3_M13F_G0f-1YLJ-3 3_M13F_H0f>1YL 1-4 1 M13F BO'-YL_l-4_2Ji113F_C0r .1yL_L4_3_M13F_D0' 13F_A06 一記事本SB文件但)端箔©格式電)查看幫助®AACCCCftACflACCTTACCAAGGCTTGACATATACCDGAACGGGCCACAAATGGTCAACTCTTTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCflGCTCGTGTCGTGAGftTGTTGGGTTAfiGTCCCGCftftCGAGCGCA

3、ACCCTCGTCGCftTCTTGCCfiCCACGTCATGGTGGGAACTCATGTGAGACTGCCGCGGTCAACTCGGAGGAAGGTGGGGATGftCGTCfififiTCATCATGCCCCTTRTGTCTTGGGCTTCftCGCATGCTfiCAATGGCGCGTACAGAG6GCTGCAAGCTAGCGATAGTGAGCGAATCCCAAAAAGCGCGTCGTftTCCGGATCGGATCTGCftftCTCGACTCCGTGAATCGGftTCGCTfiGTfiTCGCfiftTCflAflTGTTGCCGTCATACTTCCCGGGCCTTGTACACACC

4、G文件(F)筋格式(。)查看(V)幫助(H)>LysozymegDaniorerio(292620719)國MGNTESGIDIMDIDTKGASPVTASQDKLTVKGVEASKKLAAADFVRMEKYKCKIFKVAKEKDVDPALIAAIISRESRAGHTLLKGWGDHGNGFGLMQVDKRYHTPVGAnWDSEQHLTQATEILIDFIRKIKEKFPRWSLEQCVKGGIAAYNAGVNKVKSYEDVQIDEGTTGRDYANDWARAQWFKTVKDGYLL一>lysozymeg-like1Daniorerio(50540478)MGIPVILTMY

5、FLACIYGDIMKIDTTGASEVTAKQDKLTVKGVEASKKLAEHDLARMEQYKSKILmRAKQMDPAVIAAIISRESRAGAALKDGWGDHGNGFGLMQVDKRYHKLVGAWDSEEHLTQGTEILIGYIKDIKAKFPTWTKEQCFKGGISAYNAGVKNVQTYERMDVGTTGGDYANDWARAQWFKSKGY>LysozymegCtenopharyngodonideIla(194303472)MACIYGDVMKIDTTGASDSTAKQDNLTVKGVEASRKLAEHDLARMEKYKSIIIKVGRAKQMDPAVIAAIIS

6、RESRAGAALIDGWGDHGYAFGIMQIDKRYHTPVGACDSEQHITQGTEILIGFIKEIKAKFPQWTQEQCFKGGISAYNAGPGNVRTYERMDVGTAAGDYSNDWARAQWYKSKGY口二、序列導入到Mega5軟件（1）打開Mega5軟件，界面如下（2）導入需要構建系統發育樹的目的序列OK選擇分析生列類型（如果是DNA底列，點擊DNA,如果是蛋白座列，點擊Protein）出現新的對話框，創建新的數據文件選擇序列類型DNASequences|TranslatedProteinSequences|FirsttimeUser?CustomizeToolBar

7、BetaReleaseExdireTzn;IProte導入序列AlignData*：皿山yu.zj八ModelsDistanceDiversityPhylogenyUserTreeAncestors溝SeleclionTHFirsttimeUser?CustomizeToolBarBetaReleaseExoire淞I5b3:AlignaentExplorer(3回區DataEditSearchAligrunentWebSequencerDisplayKelpcUndo電CopyCtrl+C%CutCtrl+XPasteCtrltVXDeleteXDeleteGapsCtrl+DelBInse

8、rtBlankSequenceCtrl+NInsertSequenceFromFileCtrl+IaSelectSite(z),，,litiSelectSequence(s)SelectAllCtrl+AAllowBaseEditingmNA點擊SelectionFirsttimeUser?ThisisCustomizeToolBarFBelaReleaseExoiresonRates1Tuto導入序列成功。(3)序列比對分析SelectionIDRatesDNA Sequences Translated Protein Sequences |This i$First time User?Cu

9、stomize ToolB ar fBeta Release Expires： orSioeuie 與 /AbbruI. YL T-1 1 M13F A06 2 . YL 1-T 2 M1.3F 3063. YL T-l 3 M13F C064. YL 工2 1 M13F DOW 3. YL 1-2 2 M13F mOW . YL 1-2 3 M13F F067. YL 1-3 1 M13F G068. YL 1-3 2 M13F HOW9. YL 1-3 3 M13F HQ8TO. YL 1-4 L M13式m。711. YL 1-4 2 N13F 擊12. YL 1-4 3 M13F D0

10、7點擊工具欄中“w”工具，進行比對分析，比對結束后刪除兩端不能夠完全對齊堿基SelectionMI5b3:AlignuentExplorer匚叵區|DataEditSearchAligrunentWebSequencerDisplayHelp包口騫w解W的3、LjG畸必唱XXI面贏I«i；IJM耳整意刪除這FirsttimeUseCustomizeTcBetaReleaseDNASequences|TranslatedProteinSequences|J(4)系統發育分析SelectionI忘擊k*5b3:AlignmentExplorer(C:DocumerrtsandSetti.

11、一|pPfX'MtEdit&LicnmuntDupltyn«lp口CreateNerOpenReopenCloseI燃Ml1iSequences|PhyloctMticEalyxixFirsttimeU$eCustomizeTcBetaRelease胃Trtnsltit/Untrtitslata甌SelectGtrueticCodeTable2JReverseCoeplementQSaveSessionCtrlfS集ExportAlignmentyDNASequencesProteinSequences關閉窗口，選擇保存文件路徑,自定義文件名稱0MSelecbcn3:

12、AlieiuientExploroxDMASequences|FiisttimeUseSoec:wmAbbsrv1.YLITTMI3FAO2.YL工12M1.3FBO-4CustomzeT(BetaRelease3. YLIT3H13fS4. YL121Ml3m癡5. YL工-22Ml3gtEO6. YL1-23M13FFO7. YL1-31必工3mGO8. YL1-3ZM133HO9.YL1-33M13FHO10.YL：-41H1.3FBi!1，YL1-4；刀O12.YLL73M13FdSite#|437言WIth(.4三、系統發育樹構建根據不同分析目的，選擇相應的分析算法，本例子以NJ算法

13、為例Bootstrap選擇1000,點擊Compute,開始計算BEGA 5 Bet a (03 - PhyloAnalysis. BegFile Analysis HelpTArt；Align5b3z ProgresswSelectionFirst time User?Customize TooBeta Release E計算完畢后，生成系統發育樹。CA6Botaf03-PhyloAnalyais.aogQClocksModefcAtgnSelectionFir$ftimeUsee7Data巨RatesThi$i$aBETAtestreled：ePteTTutorialCuitCtfnizeTooiBaiPreie(ence$BddReleaseExoi(e$on力,月1.2010牌009Distance丞Diversity隼盅.*Ph0ogeryUseeTreeAncestorsibi15b3:TreeExplorer(C:DOCUIE*lADIIHI"lLOCALS*lTeapPhyl.目回區IImageSubtr««VimCooputQCoptionH<?lp后跑科£他虐虔隹Originaltree|Bootstrapconsensustree|58jYL141M13FB074曠LYL142M13FC07100YL143M13