Arlequin的使用说明

1、Arlequin3.1的使用说明Arlcquin功能的概述Molecular diversity分子多态性Mismatch distribution错酉己分布Haplotype frequency estimation一单倍型频率估计Linkage disequilibrium一连锁不平衡：检测不同位点上等位基因的非随机关联Hardy-Weinberg equilibrium哈温一伯梏平衡Tajima* s neutrality test-Tajima 中性检测Fu' s neutrality test Fu 中性检测Ewens-watterson neutrality test-Ew

2、ens-watiersc>n 中性检测以上三个中性检测都是基于无限位点模型，适用于DNA sequence和RFLP单倍 型。Chakrabocty' s amalgamation testChakrabocly' s 融合检测，检测人群的均一 性和同质性，和中性选择等。Minima Spanning Nctwork（MSN,最小扩张树或称之为最小支撑树，给予分子 差异。AMOVA一分子差异度分析，用以评测人群的遗传结构Parwisc genetic distances一遗传距离的估计Exact lest of population differentiation一检测随

3、机交配群体单倍型的非随机分 布Assignment test of genotype通过估计等位基因平率将单个基因型分被盗特定 的人群中。Arlcquin3.1分析的数据文件的梏式必须是以*arq为扩增名方法：用Clustalx比对后保存一个PHY梏式的文件，在PNAsp中打开该文件， 点击Generate中的Haplotype date file ,设置considered,其余的参数不变,在其 中的Generate中选其中的Arlcquin Haplotype List即可保存下用Arlcquin3.1分析 的文件的梏式（在import date中可以进行文件梏式的转换，Arlcquin的

4、数据转化 为 Arlcquin、Genepop、Biesys、phylip、Mega、WinAmova）I- j n|(x首先打开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点击。pun project,出现如下的界面:选择你要分析数据的文件，一般扩增名为*arpF面以例子中的文件加以说明:点击打开,Project tide所分析数据的名称Genotypic date输入数据是单倍型还是双倍性Gametic phase：确定输入数据中配于片段是否已知Recessi

6、ve date：确定输入数据是否为阴性Date type：输入数据的类型Missing date:缺失数据用什么字符表示对上面的例子进行数据设置点击Setting出现如下的界面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国 ?” 回=- 回二Pra)&*t | S:ruetura Bsitor - SettirQS :1CorLfaron | Prop-st

7、.viari | irroor csts点击General selling情况如下：j? Arie quin 3. 1C:/Documents and Settings/Adainistrator/®/arLequin31.Filo Vi ettf Options HalpQ Ope 3。户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 长三 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<点击Haplotype inference （单倍型频率），出现如下界面选中右侧的设置情况，如果输入的数据的形式属于配于片段已知的单倍型数据或基因型数 据，则操作界面如下 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继续设置，点击Molecular diversity indices （在分子水平上计算遗传分歧度的几个参数）设置后，出现如下图的结果Standard diversity indices:计算几种常见的分歧度参数，如等位基因的数目、分离位 点的数目、杂合的水平等.Molecular diversity indices:隔离位点的数

14、目、单倍型的数目(nh)、单倍型的多样 性(Hd)Compute minmum spanning network among haplotype:利用每个居群的单倍型数据 计算最小支撑树和最小支撑扩张网络图。Molecular distance：选择遗传距离，包括配对差异距离和核昔酸差异数的百分比。Theas (Hom):通过估计观测到的纯质性H而得到一个参数Thcata (s):通过估计观测到的隔离位点S的个数而得到的一个参数Thcata (k):通过估计观测到的等位基因K的个数Thcata (冗)通过平均配对差异数而得到的一个参数。点击Arlcquin configuration出现如下的

15、结果; Arie quin 3. 1 C:/Docu>ents andFile View Options Hdp|7| Start 回 °ause 回 Stop,三；，三 j运 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 三厂 *<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点击Browse ,选择要分析的数据，如下图点击打开如下图点击projuct wizard进行设置，这里面数据的设置，可以通过viuw project打开的文本格式来 作为参考，进行设置点击view project出现的文本格式中包含了所要设置的数据的情况MtDBAHVI.arp -记事本；_旧又文件锚小)格式杳若田帮助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设置后，出现如下的数据:点击Start,就会进行分析，将会得到一系列的结果。出现的结果在一个与原来的 文件各相同的文件夹，运行的结杲是Himi文件。AMOVA,是指对分子差异性的分析。它通

20、过对所研究居群进行不同层次的归 类和划分，可界定不同的遗传结构并进行统计学检验，从而估计出群体间、群体 内以及个体间不同层次所表现出的差异占总变异的多少，这种方法可以讨论不同 海拔高度、不同语系、以及地理群体间是否存在相应的遗传变异。Locus by locus AMOVA每个基因单独进行分子差异性的分析Include in individual level for genotypic data包括个体间金银分歧度协方差组成 和相关的固定指数。它计算出的是观察到的基因间的差异。Number of permutations用来检测方差组成和固定指数的置换数的值，如果数 值是0则不会有任何检测结果

21、。Compute minimum spanning network among haplotype 利用分子差异计算并绘制 单倍型之间的系统树。Genetic streture 中的 population comparision 选项，会出现如下的界面 Population compararion计算人群之间不相似指数（遗传距离）的大小，如Fst （短 片段的基因的遗传距离）和Nci' s （人群之间和人群内部的平均背对差异）。 Computation of Fst：计算所有配对人群的Fsl值。Rcnyolds* s distance:计算Rcnyolds' s等线性化的Fst

22、,这适合于分歧时间较短 的样本。Slatkin / s distance：计算源于配对间的Fst的Slatkin' s遗传距离。Pairwise difference：计算Nci'人群内部和人群之间的平均配对差异数。Compute relative populations：计算所有背对人群之间的相对人群大小，也可以计 算人群之间的分析时间。出现的几个界面的设置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 归 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门 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习rdy-W皂inberg Fqiiilihiium testPaifwSQ LinkagDisQQuilibcum tqstMantel testMismatch distnbutionMolecular DiversityNeutralily t

26、程stsArlequin configurationELB setting"回国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厂 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