Arlequin的使用說明

1、Arlequin3.1的使用說明Arlcquin功能的概述Molecular diversity分子多態(tài)性Mismatch distribution錯酉己分布Haplotype frequency estimation一單倍型頻率估計Linkage disequilibrium一連鎖不平衡：檢測不同位點上等位基因的非隨機關(guān)聯(lián)Hardy-Weinberg equilibrium哈溫一伯梏平衡Tajima* s neutrality test-Tajima 中性檢測Fu' s neutrality test Fu 中性檢測Ewens-watterson neutrality test-Ew

2、ens-watiersc>n 中性檢測以上三個中性檢測都是基于無限位點模型，適用于DNA sequence和RFLP單倍 型。Chakrabocty' s amalgamation testChakrabocly' s 融合檢測，檢測人群的均一 性和同質(zhì)性，和中性選擇等。Minima Spanning Nctwork（MSN,最小擴張樹或稱之為最小支撐樹，給予分子 差異。AMOVA一分子差異度分析，用以評測人群的遺傳結(jié)構(gòu)Parwisc genetic distances一遺傳距離的估計Exact lest of population differentiation一檢測隨

3、機交配群體單倍型的非隨機分 布Assignment test of genotype通過估計等位基因平率將單個基因型分被盜特定 的人群中。Arlcquin3.1分析的數(shù)據(jù)文件的梏式必須是以*arq為擴增名方法：用Clustalx比對后保存一個PHY梏式的文件，在PNAsp中打開該文件， 點擊Generate中的Haplotype date file ,設置considered,其余的參數(shù)不變,在其 中的Generate中選其中的Arlcquin Haplotype List即可保存下用Arlcquin3.1分析 的文件的梏式（在import date中可以進行文件梏式的轉(zhuǎn)換，Arlcquin的

4、數(shù)據(jù)轉(zhuǎn)化 為 Arlcquin、Genepop、Biesys、phylip、Mega、WinAmova）I- j n|(x首先打開Arlcquin3.1的界面如下: Arlequin 3. 1Jilc 7iev Dpt: ons HelpOpcr prcot . : . proot 曷 二.t: J/ c-v qj « Cq:。orct >，Start3A&o-t ：|- Cori ：-ator | >ro.八, lr-p>rt 03ta|About ArlequinArlequin ver 3.1(ci Lau-cnt Exccffier 19SS-2C0

5、6Computational and Molecular Population Genetics LabCMPGZo 3 leg cal ms:itLte. unMersrt>- of EernehttD：，cmpq unibG.ch：softwaiofarlcuin3SGOterrber 2006點擊。pun project,出現(xiàn)如下的界面:選擇你要分析數(shù)據(jù)的文件，一般擴增名為*arpF面以例子中的文件加以說明:點擊打開,Project tide所分析數(shù)據(jù)的名稱Genotypic date輸入數(shù)據(jù)是單倍型還是雙倍性Gametic phase：確定輸入數(shù)據(jù)中配于片段是否已知Recessi

6、ve date：確定輸入數(shù)據(jù)是否為陰性Date type：輸入數(shù)據(jù)的類型Missing date:缺失數(shù)據(jù)用什么字符表示對上面的例子進行數(shù)據(jù)設置點擊Setting出現(xiàn)如下的界面ArlcQum 3. 1 I.C:/Documents and Sett mca/AdaLimst rat or/4Ei/arJLcqum31.；n |xjfi la V: qv Opti one Helpq ' wm,、盥丫。 三 0 Ck>se 0。於ci國 ?” 回=- 回二Pra)&*t | S:ruetura Bsitor - SettirQS :1CorLfaron | Prop-st

7、.viari | irroor csts點擊General selling情況如下：j? Arie quin 3. 1C:/Documents and Settings/Adainistrator/®/arLequin31.Filo Vi ettf Options HalpQ Ope 3。戶t ，八 三V Vie.v resits 郎,三, L超；e C= proest Tj S：3ft 回 PF,=r 回 Stc:Satt：*3s ； Ark-su r Cor? ;.-3t : Proja5tIrrport dataSettingsGeneral settingsRwmwt Ss.

8、,e |ARLEQUIN SETTINGS O Ca eolation setingsB O Geretic structu-eOAMCVA0 Pc p i la tic n comparisonsO Popilaticn dfferentiatior Gcnotysc assignmentB E)Haplotypw inferenceELB algorithmEM algorithmEJ ：7 Linkage aisequiionim<> Hflr-VVcinbcrgO Pairwise linkage0 Martel testO Mismatch dstributicn0 Mo

9、lecuhr d versit> nd ices Neutrally testsGeneral settingsProject - e=P-o-ct ；nput ;<e:C: C<CL./veRt= m"二 Settr;= A: , strstor； z正*。三 '= Arro.p. arovahap arpResult fife：C: D?0-n-*rt2 jrs Gttrgs Acrv：-二trator 長三 re-a-2*. Exsrrpls ;4= Afro;3 srovtfsp re= 3fro.'3*3p_3 r.btrrPoyn*crp

10、b：;*Y! Controlrri3：；r-3 levs per site 10.5Tspotya:e: 75( U=sor:ror*C Ir/sr srrr ：<5t3-oe 3trc<點擊Haplotype inference （單倍型頻率），出現(xiàn)如下界面選中右側(cè)的設置情況，如果輸入的數(shù)據(jù)的形式屬于配于片段已知的單倍型數(shù)據(jù)或基因型數(shù) 據(jù)，則操作界面如下 Arlequm 3.1 C:/DocuMents and Sett mgs/Adainist rator/lBl/arlequin31.File Vi aw Opti onz Halp09淮，tV e. oro；eot 4 Ve

11、,v *e=.：t5 Ejz . e. 三(2 Co” pr：veot V| Start ® 二 回 St:>cPr©J*t I Struetura editor Settir3= I Au.r Cor. >3 u rat on I Probst .izare I Irrport eatsHso'oce -e二:ercy|7 Estimate haplotype frequencies by mere countmoSstistes eest 3 七，tB Swm，尸"or 三“m三二三三Hapbtyce ce".Riton( U=e

12、 or> 'si ce- - icon C 他三r 丫。"二石13%”nxSettingsHaplotype inference (phase known)Reset I Lose I save |ARLEQUIH SETTIHOSS Calculation settings Genetic structureO AMOVA：)Populaton comparisons<> Populaton differentiationO Genotype assienment Haplotype nTerence <> Linkage dieeuilibr

13、ium0 Hardy-Wein hereO Pairv/isc linkageO Mantel test Mismatch distributionO Molecular ervers indicesO Neutrality testsGeneral settings繼續(xù)設置，點擊Molecular diversity indices （在分子水平上計算遺傳分歧度的幾個參數(shù)）設置后，出現(xiàn)如下圖的結(jié)果Standard diversity indices:計算幾種常見的分歧度參數(shù)，如等位基因的數(shù)目、分離位 點的數(shù)目、雜合的水平等.Molecular diversity indices:隔離位點的數(shù)

14、目、單倍型的數(shù)目(nh)、單倍型的多樣 性(Hd)Compute minmum spanning network among haplotype:利用每個居群的單倍型數(shù)據(jù) 計算最小支撐樹和最小支撐擴張網(wǎng)絡圖。Molecular distance：選擇遺傳距離，包括配對差異距離和核昔酸差異數(shù)的百分比。Theas (Hom):通過估計觀測到的純質(zhì)性H而得到一個參數(shù)Thcata (s):通過估計觀測到的隔離位點S的個數(shù)而得到的一個參數(shù)Thcata (k):通過估計觀測到的等位基因K的個數(shù)Thcata (冗)通過平均配對差異數(shù)而得到的一個參數(shù)。點擊Arlcquin configuration出現(xiàn)如下的

15、結(jié)果; Arie quin 3. 1 C:/Docu>ents andFile View Options Hdp|7| Start 回 °ause 回 Stop,三；，三 j運 版,三.Log '三 0 C：o=e :ro e:tProjeot I Stfiotuf£ E:；tor 1 Settir:s 1 上.'曰二3" ？上3F，二qe，t . zsrdl In-port catsArlequin configurationU=e 3=5->03te: set-3=Ap:erc 三廠 *<eep ALOVA j 二冢Et

16、9;ormPrompt ;or *-3-：-rp=e: n'b'tkx？i-5 cstsHiiKrBw.v=e.C: Doclrents ard SettirigsVWr rinrator z > S ' ' .3fp點擊Browse ,選擇要分析的數(shù)據(jù)，如下圖點擊打開如下圖點擊projuct wizard進行設置，這里面數(shù)據(jù)的設置，可以通過viuw project打開的文本格式來 作為參考，進行設置點擊view project出現(xiàn)的文本格式中包含了所要設置的數(shù)據(jù)的情況MtDBAHVI.arp -記事本；_舊又文件錨小)格式杳若田幫助Profilelitl

17、e='ratDNA sequences in the senegalese nandenka (hyperuariable region 1)"tIData from :ttGravcn, L. f Passarino, G,Senino, 0.9 Doursot, P., Santachiara-Denerecetti, A. S. 9ttLanganey, Q，and ExcofFier, L., 1995, Evolutionary correlation betweenttcontrol region sequence and RFLP diuersitp patte

18、rn in the nitochondrial genomettoF a Senegalese sample, Hol. Biel_ Euol. 12(2):33U-3U5HbSamples-1GenotypicData=9DaSTypiDNALocusSepardtor=NONFttissingData-'?"DataSamplesSdnpluName-'Mandunka” ttReference: Grauen et al. 1995 Mol. Biol. Euol. 12:334-3* Sanipl&Si2e=119 SanpleData= <01

19、60220310QH 1ATTfiGCACCCAAAGCTAAGATTCTAfiTTTAAACTATTCTCTGTTCTTTCfiTGGGGAfiGCAGfiTTTGGGTACCACCCAAGTAl ?TCTrTCnTGCGGAnGCfiGnTnGGGIfiCCACCCfifiGTni ?TTTARACTATTCTCTGITCTrTCfiTGGGGAfiGCAGfiTTTGGGIACCfiCCCAAGTfil設置后，出現(xiàn)如下的數(shù)據(jù):點擊Start,就會進行分析，將會得到一系列的結(jié)果。出現(xiàn)的結(jié)果在一個與原來的 文件各相同的文件夾，運行的結(jié)杲是Himi文件。AMOVA,是指對分子差異性的分析。它通

20、過對所研究居群進行不同層次的歸 類和劃分，可界定不同的遺傳結(jié)構(gòu)并進行統(tǒng)計學檢驗，從而估計出群體間、群體 內(nèi)以及個體間不同層次所表現(xiàn)出的差異占總變異的多少，這種方法可以討論不同 海拔高度、不同語系、以及地理群體間是否存在相應的遺傳變異。Locus by locus AMOVA每個基因單獨進行分子差異性的分析Include in individual level for genotypic data包括個體間金銀分歧度協(xié)方差組成 和相關(guān)的固定指數(shù)。它計算出的是觀察到的基因間的差異。Number of permutations用來檢測方差組成和固定指數(shù)的置換數(shù)的值，如果數(shù) 值是0則不會有任何檢測結(jié)果

21、。Compute minimum spanning network among haplotype 利用分子差異計算并繪制 單倍型之間的系統(tǒng)樹。Genetic streture 中的 population comparision 選項，會出現(xiàn)如下的界面 Population compararion計算人群之間不相似指數(shù)（遺傳距離）的大小，如Fst （短 片段的基因的遺傳距離）和Nci' s （人群之間和人群內(nèi)部的平均背對差異）。 Computation of Fst：計算所有配對人群的Fsl值。Rcnyolds* s distance:計算Rcnyolds' s等線性化的Fst

22、,這適合于分歧時間較短 的樣本。Slatkin / s distance：計算源于配對間的Fst的Slatkin' s遺傳距離。Pairwise difference：計算Nci'人群內(nèi)部和人群之間的平均配對差異數(shù)。Compute relative populations：計算所有背對人群之間的相對人群大小，也可以計 算人群之間的分析時間。出現(xiàn)的幾個界面的設置ConfigurationAripquin 3.0Project wizardImportexportStructure editorArlcquin settingn 3.0 D:/Laurent/Arlequin/Co

23、de/TestFiles Arlequin3/DNA/mtDNAHV1.arpFie View Ophonc Helpopen project View prcjaci 4 7玲 n resuts 鼠 V玲身 Log 歸 0 Close project 回 Stan 回 修:匚 回Project ： Settngs ：| Artec tin Con:iguraton | Project v/sard mpcrt data |J SettingsArlequin calculation settingsReset I LoadSaveARLEQUIN SETTINGS Calajlation s

24、ettingB o Genctcstructjror - lOVA O Population comparisons門 Population differentiatjon G©nct/pe assignmentO Haplotype inference O Linkage disequilibriumcHarCi-WGinbergPairwise linkageO Mantel test Mismatch distribulion Molecular diversity indices Neutrality testsGeneral settingsChcoso one of th

25、e foil owing computations to GGt up:Gene田I settigsGenetic structureAMOVAPopulztiun comparisonsPopulation dtfferintEionGonctyp。assiqmMHaplotype inferenceLinkage disequilibriumH習rdy-W皂inberg Fqiiilihiium testPaifwSQ LinkagDisQQuilibcum tqstMantel testMismatch distnbutionMolecular DiversityNeutralily t

26、程stsArlequin configurationELB setting"回國Fie Yiev Qptons HelpOpen propct /vevpeect 4 Viev. resuts view Log rile 0 cose proect 0 5<art E» Pause 回 EopFrciect Settngs | Arleauin Confoiration Prefect ?/zard Import caraSettingsHaplotype inference via ELB algorithmARLEQUIN SETTINGS日 Calculatio

27、n settings日：)Genetic structure? OAMOVAO Population comparisonsO Population differentiation。Genotype assignment Haplotype inference ele aiconmm EM algorithm臼 O Linkage disequilibriumo Hardji-weinbergO Pairwise linkageO Mantel testO Mismatch disiributionO Molecular dis/ersity indices：)Neutral 曲TestsGe

28、neral settingsDirichlet pror alpha value |0.01 Epsilcn value0.01Het. site nflucncc rone; p-Gamma value;0Sampling interval|S00-No of samples:2000Burnin stepsjlOOOOORecombination steps (%). |0Use ELB olgjrthmto catrrotc gofietb phases廠 Output phase distribution fibsAM()VA settingLD settingNuutrality t

29、estOutput-g|，"tocU.d，-,"，T：，jj箝3i X | / 在»?<><«? x I.-SFWI.V RESULTS(印nw曲汕mm) Arlequn log rileH A fiun of 1S/09/C6 3t 09:29:59. SeumgShared haplctvpas口 Genetc structure>1 Locus by locusAT4OVA. F-stat bootarapfi, CJ Samples-"j '/Jithir-somplessummary司 asaaaa叫

30、XetcBSsdy>1 no. or aiieiee3 Mclacula< divfircityScariaeieaThwruOriARCBlVO1OSF1K*NayHo. o£cepiesSI4£LIO47£33?HC. O： 12C15431343。54a 4熏。.Ofu，心工e loci分3434343434WO. etpclyr led1181163zE4PseGd hcteroaygofllt71o.cooooO.QOOOOo.ocooo0.000000.00000O.15SL50.000002G.OOflOQQ.013G30.00000o.

31、ooodoO.OOOOQO.QOflOOQ.8M630.000000.00005O.45«330.4275S0.000000.00000o.ooaoogO.OOQOOO.OOOCOo.aoooo0.000000.0900D0.00300o.ooooaLO.COOOO0.00003O.OCOQOo.oaooo0.00000O.COQOO0.02CC2eO.COQOOo .口。08O.OCOQOo.oaoooO.O3IT3o.ooaooC.OOT3T70.381530.0858O.OOOQO0.000000.000000.00000c.ooooodo.oeat?Q.89SO.d323d.

32、OOOOO0.030030.000000.0000g0.00000o.oooco0.000000.000300.000000.000000.00000100.*32159O-OOOOT0.000009.000000.000000.000050.000110.000000.00003D.OOOOO0.000000.000000.000000.0000012O.COOOO0.00009Q.03CQ33.000000.00000O.COQOOC.71034ISO.COOOO0.00080.018130.000000.00000O.COOOOc.oooco1。G.OOQOQQ.308a.03603d.

33、000500.000000.00000Q.QO081=0.105010.231S30.03503o.m2M0.052470.000000.05?5410.00000O.OOOM0.000000.000000.500000.000050.0000017O.COOOO0.013430.K6BL9.826&0.03176o.coooaO.OOOC3ieO.COQOO0.0S6a.ocoaoo.oaoooo.ooooaO.COOOOc.aoQco190.021980.000030.000000.000000.00000O.COOOOO.OOOC020O.OOQOQO.OOdWO.OOOOG9.

34、S2S&o.oocoo0.000000.0000021O.COOOO0.033W0.303300.0003C0.030000.C330322O.143o90.2£3K0.019150.000000.00000O.OOOCO430.000000.000W0.009000.000000.000000.000000.01919，A八 A一。 八，八八A A -K C。A AAC,HcletTanniaAInput文件的建立：ProfileTitlc=nAn example of DNA sequence date11NbSamplcs=29Genot-picData=0Missin

35、gnata=M?Mr>ataTypc=DNALocusScparator=N()NE DataSamplesSamplcNamc= "DC1”SamplcSizc= 5LtHap7HaplOHap20SamplcData=1 G-TGAAC-TCGAT-ACG-T-TG-A-1 G-T3AACTC-AT-ACGT-T3-A-3 G-TGA-AC-TC-AT-ACG-T-TG-A-SampleNamc= MLH1HSamplcSizc= 5SamplcData=Hapl1 A-GTGAACA-TCA-T-ACG-TTGA-Hap2 1 A-GTGAACTCA-T-ACG-TTGA

36、-Hap81 G-TGAAC-TC-AT-AC G-T-TGG-A-Hapl7 1 GT-GAACTC-AT-AC-G-GTTC-A- Hap201 G-TGA-AC-TC-AT-ACG-T-TG-A-SamplcName= "LH2”SamplcSizc= 5 SamplcData=Hap61 G-TGAACTC-AT-ACGT-TCt-A-Hap122 GT-GAACTC-AT-ACG-T-TG-A-Hap35 2 A-GTGA-AC-TC-AT-ACCG-TTGGA-SamplcNamc=SamplcSizc= 5 SamplcData=Hap62(t-TCtAACTC-AT-

37、AC(t-T-T(tA-HaplO1G-TGAACTC-AT-ACGTT3-A-Hapl21GT-GAACTC-AT-ACGTTG-A-Hap251G-TGA-AC-TCGAT-AC-GT-TG-A-SamplcName= "DF2”SamplcSizc= 5 SampkData=Hap61 G-TCtAACTC-AT-ACGT-TG-A-Hap204 G-TGA-AC-TC-AT-ACG-TTG-A- SamplcNamc= MBY1HSamplcSizc= 5 SamplcData=Hapl1 A-GTGAACA-TCA-T-ACG-TTGA-Hap91 G-TGAAC-TC-A

38、T-ACAGG-ATCATGCt-A-Hap20 4 G-TGA-AC-TC-AT-ACG-T-TG-A-SamplcName= MBY2HSamplcSizc= 5 SamplcData=Hap61G-TCtAACTC-AT-ACGT-TG-A-HaplO 1 G-TGAACTC-AT-ACGT-TG-A-Hapl 81G-TGAACTC-AT-ACGT-TGGA-Hap201G-TGA-AC-TC-AT-ACG-T-TG-A-Hap261G-TGA-AC-TC-AT-TACG-T-TG-A-SampleNamc= "BY3”SamplcSizc= 5 SamplcData=Hap

39、21A-GTGAACTCA-T-AC(yT-T(tA HaplO2G-TGAACTC-AT-AC-(tT-TCt- A-Hap201G-TGA-AC-TC-AT-AC-G-TTCt-A-H叩30I1G-TGAA-C-TC-AT-AC-G-T-TG-A-fHaplOSamplcNamc= HGZ1MSamplcSizc= 5SamplcData=1 G-TGAACTC-AT-AC-Ct-T-TG-A-Hapl23GT-GAACTC-AT-AC-Ct-T-TG-A-Hap201G-TGA-AC-TC-AT-AC-G-TTG-A-fHaplOSamplcNamc= HLT1HSamplcSizc=

40、5SamplcData=1 G-TGAACTC-AT-AC-(tT-TCt- A-Hapl22GT-GAACTC-AT-AC-GTTG-A-Hap201G-TGA-AC-TC-AT-AC-G-TTt-A-Hap291GA-TGA-AC-TC-AT-ACG-TT(t-A-SamplcNamc= ”LT2”SamplcSizc= 5 SampkData=Hap20 5 G-TGA-AC-TC-AT-ACG-TTG-A-SamplcName= "ZD1”SamplcSizc= 5 SamplcData=Hap202 G-TGA-AC-TC-AT-ACG-T-TG-A-Hap221 G-TG

41、GAGAC-TC-AT-ACG-TTG-A-Hap271 G-TGA-AC-CC-AT-ACG-T-TGA-H 叩 321 AAGTGA-AC-TC-AT-ACG-TTG-A-SamplcNamc= "ZD2”SamplcSizc= 5 SampkData=HaplO1 G-TGAACTC-AT-AC GT-TG-A-Hap204 G-TGA-AC-TC-AT-ACG-TTG-A-SamplcNamc= "DZ”SamplcSizc= 5 Sampk：Data=Hapl 41 GTTGCAATCA-TC-AT-ACG-T-TG-A-Hap20 4 G-TGA-AC-TC-A

42、T-ACG-T-TG-A-SampIcNamc= "AD”SamplcSizc= 5 SamplcData=Hapl 61 GT-GAACTC-AT-AC GT-TG-AGH 叩203 G-TGA-AC-TC-AT-ACG-T-TG-A-Hap341 A-GTGA-AC-TC-AT-ACGTTG-A- SampleName= MHY1M SamplcSizc= 5 Sampk：Data=Hap3 1 A-GTGAACTCA-T-ACGT-T-TGAA-Hap20 4 G-TGA-AC-TC-AT-ACG-T-TG-A-SampleName= "GB”SamplcSizc=

43、5 SamplcData=Hap20 5 G-TGA-AC-TC-AT-ACG-T-TG-A- SamplcName= MPX1H SamplcSizc= 5 SampkData=Hap121 GT-GAACTC-AT-ACG-T-TG-A-Hap204 G-TGA-AC-TC-AT-ACG-TTG-A- SamplcNamc= “HYS” SamplcSizc= 5 SamplcData=Hapl21 GT-GAACTC-AT-ACG-T-TG-A-Hap204 G-TGA-AC-TC-AT-ACG-T-TG-A- SamplcName= “LSI” SamplcSizc= 5 Samplc

44、Data=Hapll1 GA-TGAACTC-AT-AG GT-TG-A-Hap121 GT-GAACTC-AT-AC G-T-TG-A-Hap202 G-TGA-AC-TC-AT-ACG-TTG-A-Hap291 GA-TGA-AC-TC-AT-ACGTTG-A- SamplcNamc= "MZ” SamplcSizc= 5 Sampk：Data=Hap4HaplOHapl2Hapl3Hapl9H叩4Hapl2Hap20Hap4HaplOHapl2Hapl2Hapl5Hapl6Hap20Hap21H叩23 Hap24 Hap27 Hapl5Hap20 1 AAGT3AACTCAAT-ACG-TT