生物信息学实验 系统发育树的构建

1、系统发育树的构建生物信息学生物信息学实验2内容系统发育的介绍方法综述（序列比对，构树方法）树的构建-MEGA树的可视化实例操作生物信息学实验3无根树有根树根 Root生物信息学实验4Published treesRectangular矩形的Circle圆形的Radiation辐射状的生物信息学实验5实例操作cGAS protein sequences - test.fa file和多序列比对章节同一个FASTA文件多序列比对ClustalX - test.aln, test.dnd建树Mega - .meg, .nwk, .emf, .tiffEdit tree (本课程不讲授).nwk =

2、Figtree 专业的系统发育树编辑软件.emf = Canvas 适量图作图软件生物信息学实验67 条Fasta序列，存成本地文件 test.fainv.DmeCGASMSTANHFQRILEKLSISDNERAVYTKEAEEIQNYVVDELKRVDKTFRQVFDGLSLGGSYLDRVKLNLPDEFDLHMKLKFPFDIRPTRIDQGFIYLEADLTVINPQRIHRIVLQDWLRNAFRKVFRSNQTIATTSNRVYKLTYTLEGYGCAHTILAVCGSRSISFDLVPAFEFSGSQWPFDICPVPADVSNNWPWFAIPQQKKKSAKPRTTFMVCA

3、PHWEREIMKGKDNLKNVLRLMKGLRDAHARKLPHLSSYMLKTVLLHRLESADWERDLGTLLVEMWSHLVDHLRARRLEFFLAKDHNVFNRMNQNEIKICLENASTLLRKLCIAQTCGGSYHHVAQLFNIPNinv.BfoCGAS-2MPRDAGAGKGTTSEKSGVTGKGSGKKSPDEAGATGKGSGRKSPDEAGATGKGSGRKSPDEAGATGKGSGRKTPGKPGATGKGSGRKTPKAPAATVNGSGRKTPKDATRKGSGKKSPDEAGAAGKGSGKKTPDEAGATVKGRGRKTPDESGATVKRC

4、GKKTPDEAGATGKGSCKKSPDVAGPAGKGSGRKSPVKSGATGNDRGFQTKLKKAIDNLVRVPQTDRSETAKIYNPIVRGILEEIKKIAVTEGESDIFRLQQLNSGSYFENLKVDTSNEFDFMFCIYGEKLVLQETEPDIGMVAVKLPKSSNSSLRKYLTPDGFLSPKKLLSRFRSLVERAVDTLSRAGAESPFRGLQFELTPQKDGCPAVTLMVAKKRLQISIDLVLALVAPPPWPKCTKEWKNGVTLWPNSRDIRKIKKNELHLVAKAAPPGKDPGGNKLWRLSFSQAEKDIFSGKIIN

5、PTDASHHAKTCRKDCLRCLKYIKLQLTGGVARDVDFASYHLKTVLLHAIVKQPNGWENDNLVTCIVYVIDELVQCIIKRHLPHFFIPGYNLFDPAVFRGLRHLDAVKNHFLRLNCVLQKYKRRSSLLRRLLGARKRSLENLARVENPEASHTTPIPSPHGTQQLLEVCKRGvert.GgaCGASMEETAAGRGQRRQRAARPRATRGRGTAARRGSTAREASADEQPADEASRAVVPRRTAQGGEPPVPRTLSARSRAAGGLRLREVLSQLSLGRQDVSEASGLVNHVVSHLIQAVRGRDG

6、SFSSIRRLGAGSYYEHVKISEPNEFDIMLVMPVTRLQLDESDDTGAYYYLTFKRNPKEKYLNRFLDEDGKLSAFKMLEDLRRIIKEELKHIKNVEVTVKRKKRGSPAITLLIKKPPAEISVDIILALEVQQSWPPSTQDGLNIECWLGRKVRREFRYKPIYLVAKQNKKEKLPRGNTWRLSFSHIEKAMLNNHGSIKTCCESDGVKCCRKDCLKLLKYLLERLKMKHAKELEKFCSYHVKTAFFHSCVTWPSDTDWQHENLEHCFQKYLEYFLRCLQDSQLPHFFIPQYNLLSLDDKASN

7、DFLLGQINYQLNNGFPVFHQVprot.MbrCGASMAASSPQTYTDLLREVQVPRDGKREAREAFDRAVSSLFRGEYEMLYTGSAYEGLKVKSANEFDVMAATKDWDRDMLRRKGFVVHWPPPIDAFLADVSERAEAYRNNFNRNLGRKGHAIRANGPGSLLRLNVGGVPGTTTADLVPAVPVVVDGACEPGPLSIIPDWQKKIYAIPKTRNDGRWGWRLSLSMLEKEYIRGQRNPSSKLCLRIVKYIAFEKRKLCSTKLKSYHLKMAWLAFFELKGSNFGPEGGLAGGAEVREKTKELLDF

8、MIKKVGSRSLPHFFAPNINLLCNFKQSDFNIAKAGLEAVQRVVLSLPFSmamm.AmlCGASMPANLSSFQSSLRACSAALWMRSVCFPPGDLARTGGRGSLLSRNRERKPWIPGAERPRGQLRSATPRVLAQGVKGPRADPSEHPAALGAAKCGPVGASGSRRKKSAPSSPERPQVRARTTRAKKAPLGAEDLVEGLAVPAEKMAPPAAPGPPLPRTGSRRERGARAAREQRALPEPTEVSGLGPPVPXPVPASSLRRRGAAPGAWKPRAVLEKLRLRRQEISVAAEVVNRVVDHLLRRL

9、QSCESEFKGVSLLRTGSYYEHVKISAPNEFDIMFKLEVPRIQLEEYCNSGAYYFVKFKRNPKGNPLSQFLEDEILSASKMLLKFRKIIKEEIKNIQDTDVIMEKKKRGSPAVTLLIRKPKEISVDIILALESKSSWPASTQEGLPISQWLGTKVKTNLRRQPFYLVPKHAKEGNGFQEETWRLSFSHIEKDLLKSHGHSKTCCETDGVKCCRKDCLKLMKYLLEQLKTKFGPRKELDKFCSYHVKTAFFHVCTQDPQDSHWHTRDLELCFDNCVTYFLECLKEEQLQHYFIPGFNLFSRD

10、QIDKISKEFLSQLIEYERNNGFPVFHEFmamm.MmuCGASMEDPRRRTTAPRAKKPSAKRAPTQPSRTRAHAESCGPQRGARSRRAERDGDTTEKPRAPGPRVHPARATELTKDAQPSAMDAAGATARPAVRVPQQQAILDPELPAVREPQPPADPEARKVVRGPSHRRGARSTGQPRAPRGSRKEPDKLKKVLDKLRLKRKDISEAAETVNKVVERLLRRMQKRESEFKGVEQLNTGSYYEHVKISAPNEFDVMFKLEVPRIELQEYYETGAFYLVKFKRIPRGNPLSHFLEGEVLSAT

11、KMLSKFRKIIKEEVKEIKDIDVSVEKEKPGSPAVTLLIRNPEEISVDIILALESKGSWPISTKEGLPIQGWLGTKVRTNLRREPFYLVPKNAKDGNSFQGETWRLSFSHTEKYILNNHGIEKTCCESSGAKCCRKECLKLMKYLLEQLKKEFQELDAFCSYHVKTAIFHMWTQDPQDSQWDPRNLSSCFDKLLAFFLECLRTEKLDHYFIPKFNLFSQELIDRKSKEFLSKKIEYERNNGFPIFDKLmamm.HsaCGASMQPWHGKAMQRASEAGATAPKASARNARGAPMDPTESPAAP

12、EAALPKAGKFGPARKSGSRQKKSAPDTQERPPVRATGARAKKAPQRAQDTQPSDATSAPGAEGLEPPAAREPALSRAGSCRQRGARCSTKPRPPPGPWDVPSPGLPVSAPILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQ

13、NWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF生物信息学实验7BioEdit显示多序列比对的结果生物信息学实验8Mega step 1： Convert files format to MEGASelect file Select file format Go!10Save the

14、multiple sequence alignment file (test.aln) to Mega format (test.meg)生物信息学实验11Mega 能够构建：邻接树 (Neighbor-joining, NJ tree)速度快作为练习，本课程以构建邻接树为主最大似然树 (Maximum-likelihood, ML tree)准确。但是序列多的时候，速度很慢最大简约树 (Maximum-parsimony, MP tree)最小进化树 (Minimum-evolution tree)生物信息学实验12Select Mega file生物信息学实验13Select input

15、data type:Nucleotide sequence 核苷酸序列?Protein sequence 蛋白质序列?Pairwise distance 距离矩阵?我们的例子是蛋白质序列14构建邻接树的参数 (初学者可以用默认参数)15OK, 无根邻接基因树 (unrooted NJ gene tree) 构建好了BranchNode可以双击更改基因名功能区，对树进行操作Clade / subtree生物信息学实验16Branch统计值 Bootstrap value: 表明这个位置的branch分叉成两个子branches的可信度；一般认为Boostrap value70是可靠的；或者说这个

16、位置出现这样的分叉，在进化上是稳定的。生物信息学实验17Branch length 表示这个基因从出现开始所经历的进化时间如果确定祖先基因或者设置了外群 (Outgroup)，可以将它设置为根；无根树变成了有根树Place root on branch生物信息学实验19有根邻接基因树Root is here20更改树的显示类型，默认Rectangular改成Circle看看21Circle tree在当前窗口内改变树的大小将树保存成图形文件，EMF or PDF生物信息学实验23将树保存成“树”的格式：Newick生物信息学实验24生物信息学实验25test.nwk 其实是一个文本文件，树的格式是这样的(mamm.AmlCGAS:0.19184200,mamm.HsaCGAS:0.19817878)1.0000:0.06849499,mamm.MmuCGAS:0.29393804)0.9770:0.06769174,vert.GgaCGAS:0.34079997)1.0000:0.30359084,inv.DmeCGAS:1.01095042)0.4470:0.02679967,inv.BfoCGAS-2:0.70844176,prot.MbrCGAS:0.79889828);生物信息学实验26Mega