1、序列比对

我们应用clustalw进行比对，clustalw下载连接（http://www.clustal.org/download/current/）

选择自己需要的版本

clustalw-->test.fa-->2-->1-->test.dnd-->test.aln-->X#clustalw调用该函数#test.fa输入比对数据#2选择多序列比对#1进行比对#选择输出文件*.dnd#选择输出文件*.aln#退出X

或者可以直接用MEGA7.0或者MEGA-X直接进行比对

1.1序列

1.1 序列

以7条序列为例，保存为test.fa

>WWW000001
MAADGFFATLTRCRNNHFWFTVFALFVLWYLLLYVHDWSFRISNVDTAAAATATEFIHSTENPSYFLDEPITFTHPEKIGQNPIDLIPTDEIPVPEKELK
PPALVRQRSLPNFEPPVKQRLRRNTTVENRRIKREPKRSCKNRYIYVHDLPTRFNLDFLEDCLSLSQWSDMCRYLTNSGMGPFLGNPQNLFSDTGWFITN
QFSLEVIFHNRMKQYECLTNDSSKAAAVFVPYYAGLDVARFLWGGFNTSVRDADAIGMAKWLTEKPEWKTMYGKDHFFIAGRITWDFRRGIDDDDAWGNK
LMLLPEVKNMTVLTIESSPWNENDFGIPYPTYFHPSDDGEIVNWQAKMRKIKRKTLFSFAGAPRAHLEGSIRGEVIAQCAASKRRCKLLQCGDNNLNKCY
KPFHVMKMFQGSVFCLQPPGDSYTRRSTFDSILAGCIPVFFTPGSAYVQYLWHLPRDFFKYSILIPEDDVKGKRVSIERVLSRVSRARITAMREEVIKLI
PKVVYADPRSRRLEAVEDAFDLAVKGVLERVERERRRENVSDGEFFDEEYSWKYHLFGNFEKHEWDHYFARS
>WWW000002
MGRRRPSIHDIQTVSPAFTISHISSPTNTENSFSGFSPINYHGMMAPIYGGNFADESLFLAPITATMAVANAGRDQPSAAFYPSYLPLSSPMNRNWG
>WWW000003
MKSPFEGGRICEEFTPGYYGVCAVGGMLSAGTTHLAITPLDVLKVNMQVHPVKYASIYTCFSSLLKEQGPSAFRRGWTGKFFGYGVQGACRFGLYEYFKK
VYSNVLVDQNKTVVFFISSASAEVIANVALCPFEAIKVKVQAQPHFAKGLTDGFPKLYGSEGIRGLYRGLIPLWGRNLPFSMVMFSSFEHAVDLIYRNVI
RRKKEDCSIPQQLGVTCLAGYAAGSVGSIISNPADNIVASLYNKKAESLKLAVKKIGFVNLFTRSLPIRIMLVGPVVTLQWLFYDTIKLLSGWSTSGNVI
TDTENDGAA
>WWW000004
METPAKSIADVVDEIMGIHRSLPTRPGIDEVEAAKMLIRNIEAEDQSRIEAIARQTKSKDVPEELFRILQEMQKNLVYFQSREQKREAVKLLDLDGVHEL
FDDLIQRASKCLPSSSSASSAYSRSASSRDSSSLSLENTASFSGNSLNSTTATPPVSSSSYIDKAPVKTSELYTRDDSYLKKAKGTLYSDGFRSGNASKP
QIVDSTLKPATTSGQDGEKLSLIKLASLIEASSKKGTKDLILKNKLTDQVEWLPDSIGKLSSLITLDLSENRILLLPSTIGGLSSLTTLDLHSNRLSQLP
ESIGDLLSLVHLDVSANQLTSLPSVIGRLIRLQELKLSSNLLTVLPESIGSLASLQKLDVETNDLEEFPHTIGKCSSLMEIRADYNRLKALPEAVGRISS
LEVLSVRYNNIQQLPTTMASLSSLKELDISFNQLESVPESLCFATTLVKMNISNNFADLQALPRSIGNLEMLEELNMSNNQIRVLPASFRMLSRLRVLNV
EGNPLEVPPRDVVNKGAQAVVQYMADLVENREVKSQPSISVEKLNICSFLLKMNDRYQPEM
>WWW000005
MADTGLNFNEPLNDDGMGGGVLLMKDRKIISRAQYVDSSIKMPPVWNISDLVRKEKIKSVSDMPRLYLCSAPENSHQKREWILFLGYLKEYNKVAIANID
LYELYIFPPHESLKFSHAIVYYCMEKANDVYDSQLHRASEVKSADILSEPPRLVADTSKIDGSAQTTPTSTKSFVHGRVSPLVDFKAVENKLPTDSKFPT
TGSEYAFGSRVEACRGTEPNVMVPSSCLNKNYVRTDPSYLKTLGQAHSGWMFGAIAELVDNSRDAKAAKIQISIDMICSKRAGKEIPMLSVIDDGHGMSH
QEVLRMISFGHKQPDSDDPDRIGRFGIGFKTGAMRLGRDALVLTQTVNSRSIAFLSQSLNEGKDNVEIPIVSYTRTGQIMEVDTSVQSEASAKYNLKAIK
EFSPFNKYLIGEKAGMFHENATGTQIYIWNLEEWGSSFYLEWETGMNGGSSFHQGDIYIRSRRIRSRPGQMSRTVPLDYSLRSYLEVIFLDPRMKIYLQG
SLVRSRPLAKSLNGTVVKNGCILQKPVQLTLGRCQLEREQGNCGIFLYWHGRLIEAYKRVGSMVHNGDKSHGIIGVIDVTDLMDDGKGYAWVHSNKQGFL
DSEAYALLEQWLAEISNEYLDTHVYKILLKKGNGLYKPDHEWVQCDKCRKWRMLNPGFDSKTLPQEWFCYMKPFNGKCEMPEQKIGRGVITVSAKRSGFD
TDKKLREFKDGNDEQTSYTGENSSEDSSGQTVEESTRTSLKRLRRGPPRTCRN
>WWW000006
MEINLGQLPFDIDFHPLDKLVAAGLITGDLLLYRYSADSSPQRLLEVHAHSESCRAVRFINEGHAIVTGSPDCSIIAMDVETGSVIARHENAHGAAVNRI
VNLMQSTIASGDDGGCIKIWDTRQRSCCSSFDAHEEYISDMTFASDSMKLGDGTLSVCNLRSNKIQTRSEFSEDELLSVVIMKNGRKVVCGTQTGNLLLY
SWGFFKDCSDRFVDLSPNSVDALLKLDEDRVITGSENGLISLVGILPNRIIQPIAEHSEYPVERLAFSHDRKFLGSISHDQTLKLWDLDEILEGSGNTVT
ANSTAAGTGSGSGSDSDNDEMDVDTNSLPKSSKASETKGGSKGQEGFNGFFSDL
>WWW000007
MANPGGVGSKYVSANLNKSYGQPPHHNHAPYGGSYGQAASSRTRPGGGGGGMVVLSRNRPLQKAVPKLSIPPPLNLPSLRKEHERFDPSGSTGGGYGGGG
GGGTGGGTRPTSSGMGWTKPVAAIAVEENDGSESRVVNGVDRNMNAFDGISRGSGSYMPPSAKSVTAAPSLAARATVLRGEDFPSLRAALPTTSGPVQKQ
KDNTHKKQKQTVGAESSNLQGEIYQSSLAQIHPRGQSAQRFVGNNGSKESVVGEGFERVGDQTRKQEELFPGPLPMVQLNPRSDWADDERDTGHGFSDRG
RSHELPKNESYWDRDFDIPRSSLPQKPVQNQFNNRWGQHDNNTTSAKEVSGVDPYHRNARTPSNGVGEKASSVDRDLVKENHYTQSHFTNHVIPEARQQL
NHTRDRYSTKQSSRYSSDSFHSNNSASKSSFFPSKSEGIPAKDPKPKFSFSKNEKPYSEDPFLGDERDPFSGGLLGVIKRKKDVVKQPDFHDPVRESFEA
ELERVQQMQEMERRRIVEEHERALEQARREEEERQRLIIEEEQRQRRMEEEAREAAWRVEQERVEAIQRAEELKIAREEEKKKIFMEEERRKQAAKQKLL
ELEAMMAKRQAESKNHVLDVANKKEKDDFKAVDRDEWDDSERMVERIVTSESSGSSFPNRSFEMGSSMSQSFLDRGKHVNMWRKHVFENDNTSSILVQEH
ENGLYSPDRGAYAGGGRAFPRKELYGGAGQMPSRSYYAEERAHLNEHMWSSSGGRDHYGKSRVIEIEPEFHDNLDKRYGDVEWGPSRSHSHHQPPYPGRI
YQHNEGDEIYPYGRSRYSMRQPRVLPPPSLSSMHRTSFRGENEQNKSTFMDDGLIYNHATGNESNMQIEYSDSHQEKLEPSPLLDVHEESAVAGEDEEWP
LENNEDLQGQEEYDEEENGYQEEEEAHEGDDDKIDITQEFEGLHLEDRDSPHMMDNLVLGFNEGVEVGIPSDDFERNQKNEATSNFGVPEVSVVIGDAEG
VPGDGEGLQIGSIQMPLHLHPPVGPSLTHIHPSQPPLFHFGQLRYTSPTSQGLLPVSSHYNLAQNSVPVQPTQETSAQPVVSSSHELPQENILRGLNPLP
VREIMELNVPIHEGGMDISVTGEDKKHQNTDTKVYMPLSKKRGPENQSQNAPASGEKYFSGSNSQGPFPSRGRRFGYSVRNSGMRSEASSYSDSGGFQRM
PRRVIHRTEFRIRENGDRRQSLVDDKSNSDGRGFGRSGSKRSTMSNKPLKLVVEPESSRLDPVSVQETISESRAGKGNGKEAITKSSSTHTIDLKKNDSE
EDVDAPLQSGIVRVFKQSGIEAPSDEDDFIEASLGGEASDIARSEFVVQEGQSVASKEVSTGSMTAVSQPLAPIGTPTVNPSLQDDIRSNTIKSYQTDPV
SVGSSGENDLESGALFESKNKVADDVQTASVSWDSAQINQQVMALTQTQLDEAMKSAQFDAHGATIGGHTNSGSSKPILPSSSILMKDASFSSTASPINS
LLAGEKIQFGAVTSPTVLPPSSRVVTHGVGAPDKHPNEPCVHLEDCEAGAEAAASAVAVAGITCDEIVENGLGPVTVSDVKSSGVVASDQQLGSQFRAEE
SLTVSLPADLSIETPSISLWPPLPSPPNSSTQMPSYFPGGPPPHFPYYEMNPMLGGPIYAFGPHEESSTAQSQAQKSSTAPGSGPLAPWQPCHPVVDSFY
GPPAGFTGPFVGPPGGIPGVQGPPHMVVYNHFAPVGQFGQVGLSFMGTTYIQSGKQPDWKHNPGSGMGMSDGNMDNMNMVSAQRNPANMAAPVQHLAPGS
PLLPMAMFDASPFQPASDISAQAWSRVPASPIHTLPLSQPLQQQQPALHPAQFSRGHPPVDQSLSSTTRFSDPQTSTPQQPPPPPQNNRTFPIVTDPIIT
QFPEELGLVADPATTATTTTNTTNATISQGAAGGSDNCGSHHSKDQNADIFKNRTSQGKIIPPIRQQYGQSMGYNSNYQRGGGGGGVSQKNNMGGNNHRR
VGFQGRNQQSMGVEKGFPPSKMKQVYVPKQTTGS