├── Citation.ris ├── CodeMLSrc ├── Compile Commands for Mac or Linux ├── Linux │ ├── chi2.exe │ └── codeml.exe ├── Mac │ ├── chi2.exe │ └── codeml.exe ├── Win │ ├── chi2.exe │ └── codeml.exe ├── chi2.c ├── codeml.c ├── paml.h ├── tools.c ├── treespace.c └── treesub.c ├── Custom ├── .DS_Store ├── codeml.ctl ├── dat │ ├── MtZoa.dat │ ├── cpREV10.dat │ ├── cpREV64.dat │ ├── dayhoff-dcmut.dat │ ├── dayhoff.dat │ ├── g1974a.dat │ ├── g1974c.dat │ ├── g1974p.dat │ ├── g1974v.dat │ ├── grantham.dat │ ├── jones-dcmut.dat │ ├── jones.dat │ ├── lg.dat │ ├── miyata.dat │ ├── mtArt.dat │ ├── mtREV24.dat │ ├── mtmam.dat │ └── wag.dat └── default.ctl ├── Debug_Mac.sh ├── Debug_Win.bat ├── EasyCodeML.jar ├── Example ├── .DS_Store ├── Example1.pml ├── Example1.tree ├── Example2.pml └── Example2.tre ├── Preset ├── .DS_Store ├── BM │ ├── .DS_Store │ ├── BM │ │ ├── .DS_Store │ │ └── codeml.ctl │ ├── FR │ │ ├── .DS_Store │ │ └── codeml.ctl │ └── M0 │ │ ├── .DS_Store │ │ └── codeml.ctl ├── BSM │ ├── .DS_Store │ ├── ModelA │ │ └── codeml.ctl │ └── ModelAnull │ │ ├── .DS_Store │ │ └── codeml.ctl ├── CM │ ├── .DS_Store │ ├── CmC │ │ └── codeml.ctl │ └── M22 │ │ └── codeml.ctl ├── SM │ ├── .DS_Store │ ├── M0 │ │ └── codeml.ctl │ ├── M1a │ │ └── codeml.ctl │ ├── M2a │ │ └── codeml.ctl │ ├── M3 │ │ └── codeml.ctl │ ├── M7 │ │ └── codeml.ctl │ ├── M8 │ │ └── codeml.ctl │ └── M8a │ │ └── codeml.ctl ├── chi2.exe └── codeml.exe ├── Quick_Guide.pdf ├── README.md ├── Version History.txt ├── inPath ├── .DS_Store ├── Command line for reference.txt ├── Seq1.fasta ├── Seq2.meg └── Seq3.nex └── outPath ├── .DS_Store ├── Seq1.pml ├── Seq2.pml └── Seq3.pml /Citation.ris: -------------------------------------------------------------------------------- 1 | TY - JOUR 2 | T1 - EasyCodeML: A visual tool for analysis of selection using CodeML 3 | JF - Ecology and Evolution 4 | DO - 10.1002/ece3.5015 5 | SP - 3891-3898 6 | AU - Gao, Fangluan 7 | AU - Chen, Chengjie 8 | AU - Arab, Daej A. 9 | AU - Du, Zhenguo 10 | AU - He, Yehua 11 | AU - Ho, Simon Y. W. 12 | Y1 - 2019/03/01 13 | UR - https://doi.org/10.1002/ece3.5015 14 | N2 - The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user-friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication-quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch-site, and clade models of selection. The program allows comparison of major codon-based models for analyses of selection. EasyCodeML is a stand-alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML. 15 | ER - 16 | -------------------------------------------------------------------------------- /CodeMLSrc/Compile Commands for Mac or Linux: -------------------------------------------------------------------------------- 1 | # compile commands copy from PAML packages 2 | # MAC or Linux 3 | cc -o codeml.exe -O3 codeml.c tools.c -lm 4 | cc -o chi2.exe -O3 chi2.c -lm 5 | 6 | -------------------------------------------------------------------------------- /CodeMLSrc/Linux/chi2.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Linux/chi2.exe -------------------------------------------------------------------------------- /CodeMLSrc/Linux/codeml.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Linux/codeml.exe -------------------------------------------------------------------------------- /CodeMLSrc/Mac/chi2.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Mac/chi2.exe -------------------------------------------------------------------------------- /CodeMLSrc/Mac/codeml.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Mac/codeml.exe -------------------------------------------------------------------------------- /CodeMLSrc/Win/chi2.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Win/chi2.exe -------------------------------------------------------------------------------- /CodeMLSrc/Win/codeml.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/Win/codeml.exe -------------------------------------------------------------------------------- /CodeMLSrc/chi2.c: -------------------------------------------------------------------------------- 1 | /* chi2.c 2 | cc -o chi2 chi2.c -lm 3 | cl -O2 chi2.c 4 | 5 | This program calculates the chi-square significance values for given 6 | degrees of freedom and the tail probability (type I error rate) for 7 | given observed chi-square statistic and degree of freedom. 8 | 9 | Ziheng Yang, October 1993. 10 | */ 11 | 12 | #include 13 | #include 14 | #include 15 | 16 | double QuantileChi2 (double prob, double v); 17 | 18 | #define QuantileGamma(prob,alpha,beta) QuantileChi2(prob,2.0*(alpha))/(2.0*(beta)) 19 | #define CDFGamma(x,alpha,beta) IncompleteGamma((beta)*(x),alpha,LnGammaFunction(alpha)) 20 | #define CDFChi2(x,v) CDFGamma(x,(v)/2.0,0.5) 21 | 22 | double QuantileNormal (double prob); 23 | double CDFNormal (double x); 24 | double LnGammaFunction (double alpha); 25 | double IncompleteGamma (double x, double alpha, double ln_gamma_alpha); 26 | 27 | int main(int argc, char*argv[]) 28 | { 29 | int i,j, n=20, ndf=200, nprob=8, option=0; 30 | double df, chi2, d=1.0/n, prob[]={.005, .025, .1, .5, .90, .95, .99, .999}; 31 | 32 | if (argc!=2 && argc!=3) { 33 | printf ("\n\nChi-square critical values\n"); 34 | for (i=0; ilimit) return (invers?0:1); 108 | if (x<1.28) 109 | p = .5 - x * ( .398942280444 - .399903438504 * y 110 | /(y + 5.75885480458 - 29.8213557808 111 | /(y + 2.62433121679 + 48.6959930692 112 | /(y + 5.92885724438)))); 113 | else 114 | p = 0.398942280385 * exp(-y) / 115 | (x - 3.8052e-8 + 1.00000615302 / 116 | (x + 3.98064794e-4 + 1.98615381364 / 117 | (x - 0.151679116635 + 5.29330324926 / 118 | (x + 4.8385912808 - 15.1508972451 / 119 | (x + 0.742380924027 + 30.789933034 / 120 | (x + 3.99019417011)))))); 121 | 122 | return invers ? p : 1-p; 123 | } 124 | 125 | double LnGammaFunction (double alpha) 126 | { 127 | /* returns ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places. 128 | Stirling's formula is used for the central polynomial part of the procedure. 129 | Pike MC & Hill ID (1966) Algorithm 291: Logarithm of the gamma function. 130 | Communications of the Association for Computing Machinery, 9:684 131 | */ 132 | double x=alpha, f=0, z; 133 | 134 | if (x<7) { 135 | f=1; z=x-1; 136 | while (++z<7) f*=z; 137 | x=z; f=-log(f); 138 | } 139 | z = 1/(x*x); 140 | return f + (x-0.5)*log(x) - x + .918938533204673 141 | + (((-.000595238095238*z+.000793650793651)*z-.002777777777778)*z 142 | +.083333333333333)/x; 143 | } 144 | 145 | double IncompleteGamma (double x, double alpha, double ln_gamma_alpha) 146 | { 147 | /* returns the incomplete gamma ratio I(x,alpha) where x is the upper 148 | limit of the integration and alpha is the shape parameter. 149 | returns (-1) if in error 150 | ln_gamma_alpha = ln(Gamma(alpha)), is almost redundant. 151 | (1) series expansion if (alpha>x || x<=1) 152 | (2) continued fraction otherwise 153 | RATNEST FORTRAN by 154 | Bhattacharjee GP (1970) The incomplete gamma integral. Applied Statistics, 155 | 19: 285-287 (AS32) 156 | */ 157 | int i; 158 | double p=alpha, g=ln_gamma_alpha; 159 | double accurate=1e-8, overflow=1e30; 160 | double factor, gin=0, rn=0, a=0,b=0,an=0,dif=0, term=0, pn[6]; 161 | 162 | if (x==0) return (0); 163 | if (x<0 || p<=0) return (-1); 164 | 165 | factor=exp(p*log(x)-x-g); 166 | if (x>1 && x>=p) goto l30; 167 | /* (1) series expansion */ 168 | gin=1; term=1; rn=p; 169 | l20: 170 | rn++; 171 | term*=x/rn; gin+=term; 172 | 173 | if (term > accurate) goto l20; 174 | gin*=factor/p; 175 | goto l50; 176 | l30: 177 | /* (2) continued fraction */ 178 | a=1-p; b=a+x+1; term=0; 179 | pn[0]=1; pn[1]=x; pn[2]=x+1; pn[3]=x*b; 180 | gin=pn[2]/pn[3]; 181 | l32: 182 | a++; b+=2; term++; an=a*term; 183 | for (i=0; i<2; i++) pn[i+4]=b*pn[i+2]-an*pn[i]; 184 | if (pn[5] == 0) goto l35; 185 | rn=pn[4]/pn[5]; dif=fabs(gin-rn); 186 | if (dif>accurate) goto l34; 187 | if (dif<=accurate*rn) goto l42; 188 | l34: 189 | gin=rn; 190 | l35: 191 | for (i=0; i<4; i++) pn[i]=pn[i+2]; 192 | if (fabs(pn[4]) < overflow) goto l32; 193 | for (i=0; i<4; i++) pn[i]/=overflow; 194 | goto l32; 195 | l42: 196 | gin=1-factor*gin; 197 | 198 | l50: 199 | return (gin); 200 | } 201 | 202 | 203 | double QuantileChi2 (double prob, double v) 204 | { 205 | /* returns z so that Prob{x.999998 || v<=0) return (-1); 216 | 217 | g = LnGammaFunction (v/2); 218 | xx=v/2; c=xx-1; 219 | if (v >= -1.24*log(p)) goto l1; 220 | 221 | ch=pow((p*xx*exp(g+xx*aa)), 1/xx); 222 | if (ch-e<0) return (ch); 223 | goto l4; 224 | l1: 225 | if (v>.32) goto l3; 226 | ch=0.4; a=log(1-p); 227 | l2: 228 | q=ch; p1=1+ch*(4.67+ch); p2=ch*(6.73+ch*(6.66+ch)); 229 | t=-0.5+(4.67+2*ch)/p1 - (6.73+ch*(13.32+3*ch))/p2; 230 | ch-=(1-exp(a+g+.5*ch+c*aa)*p2/p1)/t; 231 | if (fabs(q/ch-1)-.01 <= 0) goto l4; 232 | else goto l2; 233 | 234 | l3: 235 | x = QuantileNormal (p); 236 | p1=0.222222/v; ch=v*pow((x*sqrt(p1)+1-p1), 3.0); 237 | if (ch>2.2*v+6) ch=-2*(log(1-p)-c*log(.5*ch)+g); 238 | l4: 239 | q=ch; p1=.5*ch; 240 | if ((t=IncompleteGamma (p1, xx, g))<0) { 241 | printf ("\nerr IncompleteGamma"); 242 | return (-1); 243 | } 244 | p2=p-t; 245 | t=p2*exp(xx*aa+g+p1-c*log(ch)); 246 | b=t/ch; a=0.5*t-b*c; 247 | 248 | s1=(210+a*(140+a*(105+a*(84+a*(70+60*a))))) / 420; 249 | s2=(420+a*(735+a*(966+a*(1141+1278*a))))/2520; 250 | s3=(210+a*(462+a*(707+932*a)))/2520; 251 | s4=(252+a*(672+1182*a)+c*(294+a*(889+1740*a)))/5040; 252 | s5=(84+264*a+c*(175+606*a))/2520; 253 | s6=(120+c*(346+127*c))/5040; 254 | ch+=t*(1+0.5*t*s1-b*c*(s1-b*(s2-b*(s3-b*(s4-b*(s5-b*s6)))))); 255 | if (fabs(q/ch-1) > e) goto l4; 256 | 257 | return (ch); 258 | } 259 | -------------------------------------------------------------------------------- /CodeMLSrc/paml.h: -------------------------------------------------------------------------------- 1 | /* paml.h 2 | */ 3 | 4 | #if (!defined PAML_H) 5 | #define PAML_H 6 | 7 | 8 | #include 9 | #include 10 | #include 11 | #include 12 | #include 13 | #include 14 | #include 15 | #include 16 | #include 17 | 18 | #define square(a) ((a)*(a)) 19 | #define FOR(i,n) for(i=0; i(b)?(a):(b)) 24 | #define swap2(a,b,y) { y=a; a=b; b=y; } 25 | #define Pi 3.1415926535897932384626433832795 26 | 27 | #define beep putchar('\a') 28 | #define spaceming2(n) ((n)*((n)*2+9+2)*sizeof(double)) 29 | 30 | int ReadSeq (FILE *fout, FILE *fseq, int cleandata, int locus); 31 | int ScanFastaFile(FILE *f, int *ns, int *ls, int *aligned); 32 | void EncodeSeqs (void); 33 | void SetMapAmbiguity(void); 34 | void ReadPatternFreq (FILE* fout, char* fpattf); 35 | int Initialize (FILE *fout); 36 | int MoveCodonSeq (int ns, int ls, char *z[]); 37 | int PatternWeight (void); 38 | int PatternWeightJC69like (void); 39 | int PatternWeightSimple (void); 40 | int Site2Pattern (FILE *fout); 41 | 42 | double getRoot(double (*f)(double), double (*df)(double), double initVal); 43 | int f_and_x(double x[], double f[], int n, int fromx, int LastItem); 44 | void bigexp(double lnx, double *a, double *b); 45 | void SetSeed (int seed, int PrintSeed); 46 | double rndu (void); 47 | void rndu_vector (double r[], int n); 48 | void randorder(int order[], int n, int space[]); 49 | #define rnduab(a,b) ((a)+((b)-(a))*rndu()) 50 | double reflect(double x, double a, double b); 51 | #define rndexp(mean) (-(mean)*log(rndu())) 52 | double rnduM0V1 (void); 53 | double rndNormal(void); 54 | double rndBox(void); 55 | double rndAirplane(void); 56 | double rndParabola(void); 57 | double rndBactrian(void); 58 | double rndBactrianTriangle(void); 59 | double rndBactrianLaplace(void); 60 | double rndTriangle(void); 61 | double rndLaplace (void); 62 | double rndCauchy (void); 63 | double rndt2 (void); 64 | double rndt4 (void); 65 | double rndlogt2 (double loc, double s); 66 | double rndlogistic (void); 67 | double rndloglogistic (double loc, double s); 68 | double rndgamma(double alpha); 69 | double rndbeta(double p, double q); 70 | int rndpoisson(double m); 71 | int rndNegBinomial(double shape, double mean); 72 | int SampleCat (double P[], int n, double space[]); 73 | int MultiNomialAliasSetTable (int ncat, double prob[], double F[], int L[], double space[]); 74 | int MultiNomialAlias (int n, int ncat, double F[], int L[], int nobs[]); 75 | int MultiNomial2 (int n, int ncat, double prob[], int nobs[], double space[]); 76 | int DiscreteBeta (double freq[], double x[], double p, double q, int K, int UseMedian); 77 | int DiscreteGamma (double freqK[], double rK[], double alpha, double beta, int K, int UseMedian); 78 | int AutodGamma (double Mmat[], double freqK[], double rK[], double *rho1, double alfa, double rho, int K); 79 | 80 | double QuantileChi2 (double prob, double v); 81 | #define QuantileGamma(prob,alpha,beta) QuantileChi2(prob,2.0*(alpha))/(2.0*(beta)) 82 | double PDFGamma(double x, double alpha, double beta); 83 | #define CDFGamma(x,alpha,beta) IncompleteGamma((beta)*(x),alpha,LnGamma(alpha)) 84 | double PDF_InverseGamma(double x, double alpha, double beta); 85 | #define CDF_InverseGamma(x,alpha,beta) (1-CDFGamma(1/(x),alpha,beta)) 86 | #define CDFChi2(x,v) CDFGamma(x,(v)/2.0,0.5) 87 | double PDFBeta(double x, double p, double q); 88 | double CDFBeta(double x, double p, double q, double lnbeta); 89 | double QuantileBeta(double prob, double p, double q, double lnbeta); 90 | double Quantile(double(*cdf)(double x,double par[]), double p, double x, double par[], double xb[2]); 91 | double QuantileNormal (double prob); 92 | double PDFNormal (double x, double mu, double sigma2); 93 | double logPDFNormal(double x, double mu, double sigma2); 94 | double CDFNormal (double x); 95 | double logCDFNormal (double x); 96 | double PDFCauchy (double x, double m, double sigma); 97 | double PDFloglogistic (double x, double loc, double s); 98 | double PDFlogt2 (double x, double loc, double s); 99 | double PDFt2 (double x, double m, double s); 100 | double PDFt4 (double x, double m, double s); 101 | double PDFt (double x, double loc, double scale, double df, double lnConst); 102 | double CDFt (double x, double loc, double scale, double df, double lnbeta); 103 | double PDFSkewT (double x, double loc, double scale, double shape, double df); 104 | double PDFSkewN (double x, double loc, double scale, double shape); 105 | double logPDFSkewN(double x, double loc, double scale, double shape); 106 | 107 | int StirlingS2(int n, int k); 108 | double lnStirlingS2(int n, int k); 109 | double LnGamma(double alpha); 110 | #define LnBeta(p,q) (LnGamma(p) + LnGamma(q) - LnGamma(p+q)) 111 | double DFGamma(double x, double alpha, double beta); 112 | double IncompleteGamma (double x, double alpha, double ln_gamma_alpha); 113 | #define CDFBinormal(h,k,r) LBinormal(-(h),-(k),r) /* CDF for bivariate normal */ 114 | double LBinormal (double h, double k, double r); 115 | double logLBinormal (double h, double k, double r); 116 | double probBinomial (int n, int k, double p); 117 | double probBetaBinomial (int n, int k, double p, double q); 118 | double factorial (int n); 119 | double Binomial(double n, int k, double *scale); 120 | 121 | int GaussLegendreRule(const double **x, const double **w, int order); 122 | int GaussLaguerreRule(const double **x, const double **w, int order); 123 | double NIntegrateGaussLegendre(double(*fun)(double x), double a, double b, int order); 124 | 125 | int ScatterPlot (int n, int nseries, int yLorR[], double x[], double y[], 126 | int nrow, int ncol, int ForE); 127 | void rainbowRGB (double temperature, int *R, int *G, int *B); 128 | void GetIndexTernary(int *ix, int *iy, double *x, double *y, int itriangle, int K); 129 | 130 | int CodeChara (char b, int seqtype); 131 | int dnamaker (char z[], int ls, double pi[]); 132 | int picksite (char z[], int ls, int begin, int gap, char buffer[]); 133 | int transform (char z[], int ls, int direction, int seqtype); 134 | int RemoveIndel(void); 135 | int f_mono_di (FILE *fout, char z[], int ls, int iring, double fb1[], double fb2[], double CondP[]); 136 | int PickExtreme (FILE *fout, char z[], int ls, int iring, int lfrag, int ffrag[]); 137 | 138 | int print1seq (FILE*fout, unsigned char *z, int ls, int pose[]); 139 | void printSeqs(FILE *fout, int *pose, char keep[], int format); 140 | int printPatterns(FILE *fout); 141 | void printSeqsMgenes (void); 142 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, 143 | int transformed, int simple, int pose[]); 144 | int printsmaCodon (FILE *fout, unsigned char * z[], int ns, int ls, int lline, int simple); 145 | int zztox ( int n31, int l, char z1[], char z2[], double *x ); 146 | int testXMat (double x[]); 147 | double SeqDivergence (double x[], int model, double alpha, double *kapa); 148 | int symtest (double freq[], int n, int nobs, double space[], double *chisym, 149 | double* chihom); 150 | int dSdNNG1986(char *z1, char *z2, int lc, int icode, int transfed, double *dS, double *dN, double *Ssites, double *Nsites); 151 | int difcodonNG(char codon1[], char codon2[], double *SynSite,double *AsynSite, 152 | double *SynDif, double *AsynDif, int transfed, int icode); 153 | int difcodonLWL85 (char codon1[], char codon2[], double sites[3], double sdiff[3], 154 | double vdiff[3], int transfed, int icode); 155 | int testTransP (double P[], int n); 156 | double testDetailedBalance (double P[], double pi[], int n); 157 | void pijJC69 (double pij[2], double t); 158 | int PMatK80 (double P[], double t, double kapa); 159 | int PMatT92 (double P[], double t, double kappa, double pGC); 160 | int PMatTN93 (double P[], double a1t, double a2t, double bt, double pi[]); 161 | int PMatUVRoot (double P[],double t,int n,double U[],double V[],double Root[]); 162 | int PMatCijk (double PMat[], double t); 163 | int PMatQRev(double P[], double pi[], double t, int n, double space[]); 164 | int EvolveHKY85 (char source[], char target[], int ls, double t, 165 | double rates[], double pi[], double kapa, int isHKY85); 166 | double DistanceIJ (int is, int js, int model, double alpha, double *kappa); 167 | int DistanceMatNuc (FILE *fout, FILE*f2base, int model, double alpha); 168 | int EigenQREVbase (FILE* fout, double kappa[], double pi[], 169 | int *nR, double Root[], double Cijk[]); 170 | int DistanceMatNG86 (FILE *fout, FILE*fds, FILE*fdn, FILE*dt, double alpha); 171 | int setmark_61_64 (void); 172 | 173 | int BootstrapSeq (char* seqfilename); 174 | int rell(FILE*flnf, FILE*fout, int ntree); 175 | int print1site (FILE*fout, int h); 176 | int MultipleGenes (FILE* fout, FILE*fpair[], double space[]); 177 | int lfunRates (FILE* fout, double x[], int np); 178 | int AncestralSeqs (FILE *fout, double x[]); 179 | void ListAncestSeq(FILE *fout, char *zanc); 180 | int ChangesSites(FILE*fout, int coding, char *zanc); 181 | 182 | int NucListall(char b, int *nb, int ib[4]); 183 | char *getcodon(char codon[], int icodon); 184 | char *getAAstr(char *AAstr, int iaa); 185 | int Codon2AA(char codon[3], char aa[3], int icode, int *iaa); 186 | int DNA2protein(char dna[], char protein[], int lc, int icode); 187 | int printcu (FILE *f1, double fcodon[], int icode); 188 | int printcums (FILE *fout, int ns, double fcodons[], int code); 189 | int QtoPi (double Q[], double pi[], int n, double *space); 190 | int PtoPi (double P[], double pi[], int n, double *space); 191 | int PtoX (double P1[], double P2[], double pi[], double X[]); 192 | 193 | void starttimer(void); 194 | char* printtime(char timestr[]); 195 | void sleep2(int wait); 196 | char *strc (int n, int c); 197 | int printdouble(FILE*fout, double a); 198 | void strcase (char *str, int direction); 199 | void error2(char * message); 200 | int indexing(double x[], int n, int index[], int descending, int space[]); 201 | int binarysearch (const void *key, const void *base, size_t n, size_t size, int(*compare)(const void *, const void *), int *found); 202 | FILE *gfopen(char *filename, char *mode); 203 | int appendfile(FILE*fout, char*filename); 204 | 205 | int zero (double x[], int n); 206 | double sum (double x[], int n); 207 | int fillxc (double x[], double c, int n); 208 | int xtoy (double x[], double y[], int n); 209 | int abyx (double a, double x[], int n); 210 | int axtoy(double a, double x[], double y[], int n); 211 | int axbytoz(double a, double x[], double b, double y[], double z[], int n); 212 | int identity (double x[], int n); 213 | double distance (double x[], double y[], int n); 214 | double innerp(double x[], double y[], int n); 215 | double norm(double x[], int n); 216 | 217 | double Det3x3 (double x[3*3]); 218 | int matby (double a[], double b[], double c[], int n,int m,int k); 219 | int matbytransposed (double a[], double b_transposed[], double c[], int n, int m, int k); 220 | int matIout (FILE *fout, int x[], int n, int m); 221 | int matout (FILE *file, double x[], int n, int m); 222 | int matout2 (FILE *fout, double x[], int n, int m, int wid, int deci); 223 | int mattransp1 (double x[], int n); 224 | int mattransp2 (double x[], double y[], int n, int m); 225 | int matinv (double x[], int n, int m, double space[]); 226 | int matexp (double A[], int n, int nTaylorTerms, int nSquares, double space[]); 227 | #ifdef USE_GSL 228 | int matexpGSL (double A[], int n, double space[]); 229 | #endif 230 | int matsqrt (double A[], int n, double work[]); 231 | int CholeskyDecomp (double A[], int n, double L[]); 232 | int eigenQREV (double Q[], double pi[], int n, 233 | double Root[], double U[], double V[], double spacesqrtpi[]); 234 | int eigenRealSym(double A[], int n, double Root[], double work[]); 235 | 236 | int MeanVar (double x[], int n, double *mean, double *var); 237 | int variance (double x[], int n, int nx, double mx[], double vx[]); 238 | int correl (double x[], double y[], int n, double *mx, double *my, 239 | double *vxx, double *vxy, double *vyy, double *r); 240 | int comparefloat (const void *a, const void *b); 241 | int comparedouble (const void *a, const void *b); 242 | double Eff_IntegratedCorrelationTime (double x[], int n, double *mx, double *varx); 243 | int HPDinterval(double x[], int n, double HPD[2], double alpha); 244 | int DescriptiveStatistics(FILE *fout, char infile[], int nbin, int propternary, int SkipColumns); 245 | int DescriptiveStatisticsSimple (FILE *fout, char infile[], int SkipColumns); 246 | int splitline (char line[], int fields[]); 247 | int scanfile (FILE*fin, int *nrecords, int *nx, int *HasHeader, char line[], int ifields[]); 248 | 249 | double bound (int nx, double x0[], double p[], double x[], 250 | int (*testx) (double x[], int nx)); 251 | int gradient (int n, double x[], double f0, double g[], 252 | double (* fun)(double x[],int n), double space[], int Central); 253 | int Hessian (int nx, double x[], double f, double g[], double H[], 254 | double (*fun)(double x[], int n), double space[]); 255 | int HessianSKT2004 (double xmle[], double lnLm, double g[], double H[]); 256 | 257 | int H_end (double x0[], double x1[], double f0, double f1, double e1, double e2, int n); 258 | double LineSearch(double(*fun)(double x),double *f,double *x0,double xb[2],double step,double e); 259 | double LineSearch2 (double(*fun)(double x[],int n), double *f, double x0[], 260 | double p[], double h, double limit, double e, double space[], int n); 261 | 262 | void xtoFreq(double x[], double freq[], int n); 263 | 264 | 265 | int SetxBound (int np, double xb[][2]); 266 | int ming1 (FILE *fout, double *f, double (* fun)(double x[], int n), 267 | int (*dfun) (double x[], double *f, double dx[], int n), 268 | int (*testx) (double x[], int n), 269 | double x0[], double space[], double e, int n); 270 | int ming2 (FILE *fout, double *f, double (*fun)(double x[], int n), 271 | int (*dfun)(double x[], double *f, double dx[], int n), 272 | double x[], double xb[][2], double space[], double e, int n); 273 | int minB (FILE*fout, double *lnL,double x[],double xb[][2],double e, double space[]); 274 | int minB2 (FILE*fout, double *lnL,double x[],double xb[][2],double e, double space[]); 275 | 276 | 277 | int Newton (FILE *fout, double *f, double (* fun)(double x[], int n), 278 | int (* ddfun) (double x[], double *fx, double dx[], double ddx[], int n), 279 | int (*testx) (double x[], int n), 280 | double x0[], double space[], double e, int n); 281 | 282 | int nls2 (FILE *fout, double *sx, double * x0, int nx, 283 | int (* fun)(double x[], double y[], int nx, int ny), 284 | int (* jacobi)(double x[], double J[], int nx, int ny), 285 | int (*testx) (double x[], int nx), 286 | int ny, double e); 287 | 288 | int ResetFinetuneSteps(FILE *fout, double Pjump[], double finetune[], int nsteps); 289 | 290 | /* tree structure functions in treesub.c */ 291 | void NodeToBranch (void); 292 | void BranchToNode (void); 293 | void ClearNode (int inode); 294 | int ReadTreeN (FILE *ftree, int *haslength, int *haslabel, int copyname, int popline); 295 | int ReadTreeB (FILE *ftree, int popline); 296 | int OutTreeN (FILE *fout, int spnames, int printopt); 297 | int OutTreeB (FILE *fout); 298 | int DeRoot (void); 299 | int GetSubTreeN (int keep[], int space[]); 300 | void printtree (int timebranches); 301 | void PointconPnodes (void); 302 | int SetBranch (double x[]); 303 | int DistanceMat (FILE *fout, int ischeme, double alfa, double *kapa); 304 | int LSDistance (double * ss, double x[], int (*testx)(double x[],int np)); 305 | 306 | int StepwiseAdditionMP (double space[]); 307 | double MPScoreStepwiseAddition (int is, double space[], int save); 308 | int AddSpecies (int species, int ib); 309 | int StepwiseAddition (FILE* fout, double space[]); 310 | int readx(double x[], int *fromfile); 311 | double TreeScore(double x[], double space[]); 312 | 313 | int PopEmptyLines (FILE* fseq, int lline, char line[]); 314 | int hasbase (char *str); 315 | int blankline (char *str); 316 | 317 | void BranchLengthBD(int rooted, double birth, double death, double sample, 318 | double mut); 319 | int RandomLHistory (int rooted, double space[]); 320 | 321 | void Tree2Partition (char partition[]); 322 | int Partition2Tree (char splits[], int lsplit, int ns, int nsplit, double label[]); 323 | void CladeSupport (FILE *fout, char treef[], int getSnames, char mastertreef[], int pick1tree); 324 | int GetNSfromTreeFile(FILE *ftree, int *ns, int *ntree); 325 | int NSameBranch (char partition1[],char partition2[], int nib1,int nib2, int IBsame[]); 326 | 327 | int QTN93 (int model, double Q[], double kappa1, double kappa2, double pi[]); 328 | int RootTN93 (int ischeme, double kapa1, double kapa2, double pi[], double *scalefactor, double Root[]); 329 | int EigenTN93 (int ischeme, double kapa1, double kapa2, double pi[], int *nR, double Root[], double Cijk[]); 330 | 331 | int DownStatesOneNode (int ison, int father); 332 | int DownStates (int inode); 333 | int PathwayMP (FILE *fout, double space[]); 334 | double MPScore (double space[]); 335 | double RemoveMPNinfSites (double *nsiteNinf); 336 | int MarkStopCodons(void); 337 | 338 | int MPInformSites (void); 339 | int CollapsNode (int inode, double x[]); 340 | 341 | int MakeTreeIb (int ns, int Ib[], int rooted); 342 | int GetTreeI (int itree, int ns, int rooted); 343 | double CountTrees (int ns, int rooted); 344 | double CountLHs (int ns); 345 | int CountLHsTree (void); 346 | int ListTrees (FILE* fout, int ns, int rooted); 347 | int GetIofTree (int rooted, int keeptree, double space[]); 348 | void ReRootTree (int newroot); 349 | int NeighborNNI (int i_tree); 350 | int GetLHistoryI (int iLH); 351 | int GetIofLHistory (void); 352 | int CountLHistory(char LHistories[], double space[]); 353 | int ReorderNodes (char LHistory[]); 354 | 355 | int GetSubSeqs(int nsnew); 356 | 357 | /* functions for evolving sequences */ 358 | int GenerateSeq (void); 359 | int Rates4Sites (double rates[],double alfa,int ncatG,int ls, int cdf, 360 | double space[]); 361 | void Evolve (int inode); 362 | void EvolveJC (int inode); 363 | 364 | 365 | int ReadTreeSeqs(FILE*fout); 366 | int UseLocus (int locus, int copyconP, int setmodel, int setSeqName); 367 | int GetGtree(int locus); 368 | int printGtree(int printBlength); 369 | 370 | void copySptree(void); 371 | void printSptree(void); 372 | 373 | 374 | enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; 375 | 376 | enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; 377 | 378 | 379 | /* use mean (0; default) for discrete gamma instead of median (1) */ 380 | #define DGammaUseMedian 0 381 | 382 | 383 | #define FAST_RANDOM_NUMBER 384 | 385 | #define mBactrian 0.95 386 | #define sBactrian sqrt(1-mBactrian*mBactrian) 387 | #define aBox 0.5 388 | #define bBox (sqrt(12 - 3*aBox*aBox) - aBox) / 2 389 | #define aAirplane 1.0 390 | #define aParab 1.0 391 | 392 | 393 | #define MAXNFIELDS 320000 394 | 395 | #define PAML_RELEASE 0 396 | 397 | #define FullSeqNames 0 /* 1: numbers at the beginning of sequence name are part of name */ 398 | 399 | #define pamlVerStr "paml version 4.9, March 2015" 400 | 401 | #endif 402 | -------------------------------------------------------------------------------- /CodeMLSrc/tools.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/CodeMLSrc/tools.c -------------------------------------------------------------------------------- /CodeMLSrc/treespace.c: -------------------------------------------------------------------------------- 1 | /* treespace.c 2 | collection of tree perturbation routines 3 | */ 4 | 5 | #include "paml.h" 6 | 7 | int MakeTreeIb (int ns, int Ib[], int rooted) 8 | { 9 | /* construct tree from Ib[] using the algorithm of adding species 10 | Ib[k] marks the branch to which the (k+3)_th species (or the root) 11 | is added. Ib[k] should be in the range [0,k+3] 12 | */ 13 | int i,j,k, is,it; 14 | 15 | tree.nbranch=3; 16 | for (i=0; i<3; i++) { tree.branches[i][0]=3; tree.branches[i][1]=i; } 17 | for (k=0; k=is) tree.branches[i][j]+=2; 22 | it=tree.branches[Ib[k]][1]; 23 | tree.branches[Ib[k]][1]=is+1; 24 | tree.branches[tree.nbranch][0]=is+1; 25 | tree.branches[tree.nbranch++][1]=it; 26 | tree.branches[tree.nbranch][0]=is+1; 27 | tree.branches[tree.nbranch++][1]=is; 28 | } 29 | tree.root=tree.branches[0][0]; 30 | BranchToNode (); 31 | 32 | if (rooted) { 33 | it=tree.branches[Ib[k]][0]; 34 | tree.branches[Ib[k]][0]=tree.branches[tree.nbranch][0]=2*com.ns-2; 35 | tree.branches[tree.nbranch][1]=it; 36 | for (; it!=tree.root; it=nodes[it].father) { 37 | tree.branches[nodes[it].ibranch][0]=it; 38 | tree.branches[nodes[it].ibranch][1]=nodes[it].father; 39 | } 40 | tree.root=2*com.ns-2; tree.nbranch++; 41 | BranchToNode (); 42 | } 43 | return (0); 44 | } 45 | 46 | int GetTreeI (int itree, int ns, int rooted) 47 | { 48 | /* get the i_th tree. Trees are ordered according to the algorithm of 49 | adding species. 50 | returns a random tree if itree==-1, in which case ns can be large 51 | */ 52 | int i, M[NS-2], nM=ns-3+rooted, Ib[NS-2]; 53 | 54 | for (i=0; i3) { 61 | FOR (i, nM) printf ("%5d ", M[i]); FPN (F0); 62 | FOR (i, nM) printf ("%5d ", Ib[i]); FPN (F0); 63 | } 64 | */ 65 | MakeTreeIb (ns, Ib, rooted); 66 | return (0); 67 | } 68 | 69 | 70 | 71 | int CountLHsTree (void) 72 | { 73 | /* This counts the number of labeled histories for a given rooted tree. 74 | */ 75 | int i,k, nLH, nLR[NS-1][2], change, *sons, j; 76 | double y=0; 77 | 78 | for(i=com.ns; i=com.ns; i--) { 84 | sons = nodes[i].sons; 85 | for(j=0; j<2; j++) { 86 | if(nLR[i-com.ns][j] != -1) continue; 87 | if(sons[j] < com.ns) { 88 | nLR[i-com.ns][j] = 0; 89 | change = 1; 90 | } 91 | else if(nLR[sons[j]-com.ns][0] != -1 && nLR[sons[j]-com.ns][1] != -1) { 92 | nLR[i-com.ns][j] = nLR[sons[j]-com.ns][0] + nLR[sons[j]-com.ns][1] + 1; 93 | change = 1; 94 | } 95 | } 96 | } 97 | if(!change) break; 98 | } 99 | for(i=0,nLH=1; i=0; i--) { 143 | if (Ib[i]<2*i+3) break; 144 | if (i==0) { 145 | finish=1; 146 | break; 147 | } 148 | Ib[i]=0; Ib[i-1]++; 149 | } 150 | if (finish) break; 151 | } 152 | FPN(fout); 153 | 154 | return (0); 155 | } 156 | 157 | int GetIofTree (int rooted, int keeptree, double space[]) 158 | { 159 | /* Get the index of tree. 160 | tree.branches[] are destroyed for reconstruction, 161 | and some branches are reversed which may affect nodes[] also. 162 | Both are restored before return if keeptree=1. 163 | Works with binary trees only. 164 | bA[nbranch*(ns-2)] 165 | */ 166 | int M[NS-2], nM=com.ns-3+rooted; 167 | int i,j,k,is,it, b=0,a1,a2,Ib[NS-1], nid=tree.nnode-com.ns; 168 | char ns2=(char)(com.ns-2), *bA=(char*)space; /* bA[b*ns2+j]: ancestors on branch b */ 169 | struct TREEB tree0=tree; 170 | 171 | if (tree.nnode-com.ns!=com.ns-1-!rooted) error2 ("GetIofTree"); 172 | if (com.ns>15) error2("ns too large in GetIofTree"); 173 | 174 | /* find new root. 175 | Ib[]: No. of times inner nodes are visited on paths 1-2, 1-3, 2-3 */ 176 | for (i=0; ib becomes b->a */ 243 | 244 | if (newroot==oldroot) return; 245 | for (b=newroot,a=nodes[b].father; b!=oldroot; b=a,a=nodes[b].father) { 246 | tree.branches[nodes[b].ibranch][0]=b; 247 | tree.branches[nodes[b].ibranch][1]=a; 248 | #if (BASEML || CODEML) 249 | if(a>=com.ns /* && com.method==1 */) com.oldconP[a]=0; /* update the node */ 250 | #endif 251 | } 252 | 253 | tree.root=newroot; 254 | BranchToNode (); 255 | for (b=oldroot,a=nodes[b].father; b!=newroot; b=a,a=nodes[b].father) { 256 | nodes[b].branch = nodes[a].branch; 257 | nodes[b].label = nodes[a].label; 258 | } 259 | nodes[newroot].branch = -1; 260 | nodes[newroot].label = -1; 261 | 262 | #if (CODEML) 263 | /* omega's are moved in updateconP for NSbranchsites models */ 264 | if(com.model && com.NSsites==0) { 265 | for (b=oldroot,a=nodes[b].father; b!=newroot; b=a,a=nodes[b].father) 266 | nodes[b].omega = nodes[a].omega; 267 | nodes[newroot].omega = -1; 268 | } 269 | #endif 270 | #if (BASEML) 271 | if(com.nhomo==2) { 272 | for (b=oldroot,a=nodes[b].father; b!=newroot; b=a,a=nodes[b].father) 273 | nodes[b].pkappa = nodes[a].pkappa; 274 | nodes[newroot].pkappa = NULL; 275 | } 276 | #endif 277 | 278 | } 279 | 280 | 281 | 282 | int NeighborNNI (int i_tree) 283 | { 284 | /* get the i_tree'th neighboring tree of tree by the nearest neighbor 285 | interchange (NNI), each tree has 2*(# internal branches) neighbors. 286 | works with rooted and unrooted binary trees. 287 | 288 | Gives the ip_th neighbor for interior branch ib. 289 | Involved branches are a..b, a..c, b..d, 290 | with a..b to be the internal branch. 291 | swap c with d, with d to be the ip_th son of b 292 | */ 293 | int i, a,b,c,d, ib=i_tree/2, ip=i_tree%2; 294 | 295 | if (tree.nbranch!=com.ns*2-2-(nodes[tree.root].nson==3)) 296 | error2 ("err NeighborNNI: multificating tree."); 297 | 298 | /* locate a,b,c,d */ 299 | for (i=0,a=0; i=com.ns && a++==ib) break; 301 | ib=i; 302 | a=tree.branches[ib][0]; b=tree.branches[ib][1]; 303 | c=nodes[a].sons[0]; if(c==b) c=nodes[a].sons[1]; 304 | d=nodes[b].sons[ip]; 305 | 306 | /* swap nodes c and d */ 307 | tree.branches[nodes[c].ibranch][1]=d; 308 | tree.branches[nodes[d].ibranch][1]=c; 309 | BranchToNode (); 310 | return (0); 311 | } 312 | 313 | int GetLHistoryI (int iLH) 314 | { 315 | /* Get the ILH_th labelled history. This function is rather similar to 316 | GetTreeI which returns the I_th rooted or unrooted tree topology. 317 | The labeled history is recorded in the numbering of nodes: 318 | node # increases as the node gets older: 319 | node d corresponds to time 2*ns-2-d; tree.root=ns*2-2; 320 | t0=1 > t1 > t2 > ... > t[ns-2] 321 | k ranges from 0 to i(i-1)/2 and indexes the pair (s1 & s2, with s1=2; i--) { 332 | k=it%(i*(i-1)/2); it/=(i*(i-1)/2); 333 | s2=(int)(sqrt(1.+8*k)-1)/2+1; s1=k-s2*(s2-1)/2; /* s1=s2 || s1<0) printf("\nijk%6d%6d%6d", s1, s2, k); 336 | 337 | nodes[nodea[s1]].father=nodes[nodea[s2]].father=inode; 338 | nodes[inode].nson=2; 339 | nodes[inode].sons[0]=nodea[s1]; 340 | nodes[inode].sons[1]=nodea[s2]; 341 | nodea[s1]=inode; nodea[s2]=nodea[i-1]; 342 | inode++; 343 | } 344 | tree.root=inode-1; 345 | NodeToBranch(); 346 | return (0); 347 | } 348 | 349 | int GetIofLHistory (void) 350 | { 351 | /* Get the index of the labelled history (rooted tree with nodes ordered 352 | according to time). 353 | Numbering of nodes: node # increases as the node gets older: 354 | node d corresponds to time 2*ns-2-d; tree.root=ns*2-2; 355 | t0=1 > t1 > t2 > ... > t[ns-2] 356 | */ 357 | int index, i,j,k[NS+1], inode,nnode, nodea[NS], s[2]; 358 | 359 | if (nodes[tree.root].nson!=2 || tree.nnode!=com.ns*2-1 360 | || tree.root!=com.ns*2-2) error2("IofLH"); 361 | for (i=0; i=com.ns) 392 | FOR (k, com.ns-1) 393 | if (tree.branches[i][j]==LHistory[k]) 394 | { tree.branches[i][j]=com.ns*2-2-k; break; } 395 | BranchToNode(); 396 | 397 | return (0); 398 | } 399 | -------------------------------------------------------------------------------- /Custom/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Custom/.DS_Store -------------------------------------------------------------------------------- /Custom/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = 2 | treefile = 3 | outfile = 4 | noisy = 9 5 | verbose = 0 6 | runmode = 0 7 | icode = 0 8 | fix_omega = 0 9 | ncatG = 4 10 | fix_alpha = 0 11 | ndata = 1 12 | clock = 0 13 | seqtype = 2 14 | aaRatefile = dat/wag.dat 15 | fix_blength = 0 16 | omega = 2 17 | Mgene = 0 18 | Small_Diff = .5e-6 19 | getSE = 0 20 | RateAncestor = 1 21 | alpha = 0.5 22 | fix_kappa = 0 23 | model = 2 24 | kappa = 2 25 | CodonFreq = 2 26 | aaDist = 0 27 | cleandata = 1 28 | Malpha = 1 29 | -------------------------------------------------------------------------------- /Custom/dat/MtZoa.dat: -------------------------------------------------------------------------------- 1 | 2 | 3.3 3 | 1.7 33.6 4 | 16.1 3.2 617.0 5 | 272.5 61.1 94.6 9.5 6 | 7.3 231.0 190.3 19.3 49.1 7 | 17.1 6.4 174.0 883.6 3.4 349.4 8 | 289.3 7.2 99.3 26.0 82.4 8.9 43.1 9 | 2.3 61.7 228.9 55.6 37.5 421.8 14.9 7.4 10 | 33.2 0.2 24.3 1.5 48.8 0.2 7.3 3.4 1.6 11 | 15.6 4.1 7.9 0.5 59.7 23.0 1.0 3.5 6.6 425.2 12 | 0.2 292.3 413.4 0.2 0.2 334.0 163.2 10.1 23.9 8.4 6.7 13 | 136.5 3.8 73.7 0.2 264.8 83.9 0.2 52.2 7.1 449.7 636.3 83.0 14 | 26.5 0.2 12.9 2.0 167.8 9.5 0.2 5.8 13.1 90.3 234.2 16.3 215.6 15 | 61.8 7.5 22.6 0.2 8.1 52.2 20.6 1.3 15.6 2.6 11.4 24.3 5.4 10.5 16 | 644.9 11.8 420.2 51.4 656.3 96.4 38.4 257.1 23.1 7.2 15.2 144.9 95.3 32.2 79.7 17 | 378.1 3.2 184.6 2.3 199.0 39.4 34.5 5.2 19.4 222.3 50.0 75.5 305.1 19.3 56.9 666.3 18 | 3.1 16.9 6.4 0.2 36.1 6.1 3.5 12.3 4.5 9.7 27.2 6.6 48.7 58.2 1.3 10.3 3.6 19 | 2.1 13.8 141.6 13.9 76.7 52.3 10.0 4.3 266.5 13.1 5.7 45.0 41.4 590.5 4.2 29.7 29.0 79.8 20 | 321.9 5.1 7.1 3.7 243.8 9.0 16.3 23.7 0.3 1710.6 126.1 11.1 279.6 59.6 17.9 49.5 396.4 13.7 15.6 21 | 22 | 0.068880 0.021037 0.030390 0.020696 0.009966 0.018623 0.024989 0.071968 0.026814 0.085072 0.156717 0.019276 0.050652 0.081712 0.044803 0.080535 0.056386 0.027998 0.037404 0.066083 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 25 | // end of file 26 | 27 | Rota-Stabelli, O., Z. Yang, and M. Telford. 2009. MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol. Phyl. Evol. 28 | -------------------------------------------------------------------------------- /Custom/dat/cpREV10.dat: -------------------------------------------------------------------------------- 1 | 2 | 105 3 | 227 357 4 | 175 43 4435 5 | 669 823 538 10 6 | 157 1745 768 400 10 7 | 499 152 1055 3691 10 3122 8 | 665 243 653 431 303 133 379 9 | 66 715 1405 331 441 1269 162 19 10 | 145 136 168 10 280 92 148 40 29 11 | 197 203 113 10 396 286 82 20 66 1745 12 | 236 4482 2430 412 48 3313 2629 263 305 345 218 13 | 185 125 61 47 159 202 113 21 10 1772 1351 193 14 | 68 53 97 22 726 10 145 25 127 454 1268 72 327 15 | 490 87 173 170 285 323 185 28 152 117 219 302 100 43 16 | 2440 385 2085 590 2331 396 568 691 303 216 516 868 93 487 1202 17 | 1340 314 1393 266 576 241 369 92 32 1040 156 918 645 148 260 2151 18 | 14 230 40 18 435 53 63 82 69 42 159 10 86 468 49 73 29 19 | 56 323 754 281 1466 391 142 10 1971 89 189 247 215 2370 97 522 71 346 20 | 968 92 83 75 592 54 200 91 25 4797 865 249 475 317 122 167 760 10 119 21 | 22 | 0.0755 0.0621 0.0410 0.0371 0.0091 0.0382 0.0495 0.0838 0.0246 0.0806 23 | 0.1011 0.0504 0.0220 0.0506 0.0431 0.0622 0.0543 0.0181 0.0307 0.0660 24 | 25 | A R N D C Q E G H I L K M F P S T W Y V 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | Symmetrical part of the rate matrix and aa frequencies, estimated for 29 | plant chloroplast proteins, under the REVaa model. The first part is 30 | S_ij = S_ji, and the second part has the amino acid frequencies 31 | (\pi_i). The substitution rate from amino acid i to j is Q_ij = 32 | S_ij*PI_j. This is the cpREV model used in protml 2.3b6 (12/10/98), 33 | described by 34 | 35 | Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa. 2000. Plastid 36 | genome phylogeny and a model of amino acid substitution for proteins 37 | encoded by chloroplast DNA. Journal of Molecular Evolution 50:348-358. 38 | 39 | 40 | protml 2.3b6 (12/10/98) cpREV45 6 OTUs 1344 sites. 41 | 42 | Relative Substitution Rate Matrix 43 | Ala 105 227 175 669 157 499 665 66 145 197 236 185 68 490 2440 1340 14 56 968 44 | 105 Arg 357 43 823 1745 152 243 715 136 203 4482 125 53 87 385 314 230 323 92 45 | 227 357 Asn 4435 538 768 1055 653 1405 168 113 2430 61 97 173 2085 1393 40 754 83 46 | 175 43 4435 Asp 10 400 3691 431 331 10 10 412 47 22 170 590 266 18 281 75 47 | 669 823 538 10 Cys 10 10 303 441 280 396 48 159 726 285 2331 576 435 1466 592 48 | 157 1745 768 400 10 Gln 3122 133 1269 92 286 3313 202 10 323 396 241 53 391 54 49 | 499 152 1055 3691 10 3122 Glu 379 162 148 82 2629 113 145 185 568 369 63 142 200 50 | 665 243 653 431 303 133 379 Gly 19 40 20 263 21 25 28 691 92 82 10 91 51 | 66 715 1405 331 441 1269 162 19 His 29 66 305 10 127 152 303 32 69 1971 25 52 | 145 136 168 10 280 92 148 40 29 Ile 1745 345 1772 454 117 216 1040 42 89 4797 53 | 197 203 113 10 396 286 82 20 66 1745 Leu 218 1351 1268 219 516 156 159 189 865 54 | 236 4482 2430 412 48 3313 2629 263 305 345 218 Lys 193 72 302 868 918 10 247 249 55 | 185 125 61 47 159 202 113 21 10 1772 1351 193 Met 327 100 93 645 86 215 475 56 | 68 53 97 22 726 10 145 25 127 454 1268 72 327 Phe 43 487 148 468 2370 317 57 | 490 87 173 170 285 323 185 28 152 117 219 302 100 43 Pro 1202 260 49 97 122 58 | 2440 385 2085 590 2331 396 568 691 303 216 516 868 93 487 1202 Ser 2151 73 522 167 59 | 1340 314 1393 266 576 241 369 92 32 1040 156 918 645 148 260 2151 Thr 29 71 760 60 | 14 230 40 18 435 53 63 82 69 42 159 10 86 468 49 73 29 Trp 346 10 61 | 56 323 754 281 1466 391 142 10 1971 89 189 247 215 2370 97 522 71 346 Tyr 119 62 | 968 92 83 75 592 54 200 91 25 4797 865 249 475 317 122 167 760 10 119 Val 63 | 64 | Instantaneous Rate Matrix (x1.0e7) 65 | -91529 1244 1785 1237 1154 1146 4685 10703 317 2255 66 | 1525 -89950 2801 308 1418 12704 1430 3915 3425 2104 67 | 3308 4236 -148182 31435 928 5592 9901 10512 6730 2610 68 | 2541 516 34834 -102527 17 2913 34646 6941 1585 155 69 | 9744 9769 4227 71 -104875 73 94 4875 2113 4351 70 | 2291 20728 6034 2836 17 -122138 29310 2147 6078 1425 71 | 7267 1809 8285 26162 17 22730 -119787 6093 775 2300 72 | 9684 2890 5131 3057 522 971 3554 -40638 91 622 73 | 964 8494 11037 2345 761 9239 1519 306 -58046 447 74 | 2116 1611 1321 71 483 669 1391 645 138 -133037 75 | 2864 2412 890 71 683 2085 768 322 318 27085 76 | 3436 53232 19085 2918 82 24119 24682 4239 1463 5361 77 | 2698 1479 482 332 274 1470 1061 331 48 27490 78 | 992 629 760 159 1252 73 1359 398 609 7045 79 | 7129 1034 1355 1206 491 2354 1740 456 727 1817 80 | 35520 4578 16378 4179 4018 2879 5336 11116 1453 3346 81 | 19503 3730 10942 1883 994 1755 3467 1474 155 16143 82 | 210 2728 313 126 749 384 595 1315 330 654 83 | 814 3832 5922 1994 2528 2848 1334 161 9438 1383 84 | 14095 1096 649 528 1020 394 1876 1464 118 74430 85 | 86 | 3806 2261 781 666 4033 28977 13857 50 332 12240 87 | 3929 42929 525 518 717 4578 3249 792 1916 1167 88 | 2192 23275 259 946 1421 24766 14411 137 4477 1045 89 | 193 3943 198 220 1402 7002 2747 61 1670 942 90 | 7660 458 669 7094 2348 27681 5962 1499 8708 7480 91 | 5541 31736 851 98 2663 4698 2495 182 2324 684 92 | 1584 25185 476 1415 1527 6752 3820 219 844 2527 93 | 388 2523 87 242 233 8204 947 282 59 1150 94 | 1284 2925 42 1243 1250 3603 335 238 11703 311 95 | 33772 3309 7466 4436 965 2561 10762 145 529 60646 96 | -79825 2086 5695 12392 1807 6129 1610 548 1124 10936 97 | 4214 -171296 815 704 2488 10315 9498 34 1469 3142 98 | 26146 1852 -83052 3193 825 1109 6672 298 1280 6012 99 | 24541 690 1377 -67258 358 5784 1532 1613 14072 4013 100 | 4244 2893 422 425 -45559 14281 2690 170 577 1548 101 | 9985 8318 394 4758 9904 -149879 22249 251 3101 2115 102 | 3011 8795 2718 1447 2142 25545 -113841 100 424 9613 103 | 3076 96 364 4570 405 864 300 -19261 2055 126 104 | 3661 2369 908 23151 800 6202 738 1193 -70777 1500 105 | 16736 2380 2004 3101 1009 1987 7865 34 705 -131490 106 | 107 | Instantaneous Rate Matrix (x1.0e5) 108 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 109 | Ala 99085 12 18 12 12 11 47 107 3 23 38 23 8 7 40 290 139 0 3 122 110 | Arg 15 99100 28 3 14 127 14 39 34 21 39 429 5 5 7 46 32 8 19 12 111 | Asn 33 42 98518 314 9 56 99 105 67 26 22 233 3 9 14 248 144 1 45 10 112 | Asp 25 5 348 98975 0 29 346 69 16 2 2 39 2 2 14 70 27 1 17 9 113 | Cys 97 98 42 1 98951 1 1 49 21 44 77 5 7 71 23 277 60 15 87 75 114 | Gln 23 207 60 28 0 98779 293 21 61 14 55 317 9 1 27 47 25 2 23 7 115 | Glu 73 18 83 262 0 227 98802 61 8 23 16 252 5 14 15 68 38 2 8 25 116 | Gly 97 29 51 31 5 10 36 99594 1 6 4 25 1 2 2 82 9 3 1 12 117 | His 10 85 110 23 8 92 15 3 99420 4 13 29 0 12 13 36 3 2 117 3 118 | Ile 21 16 13 1 5 7 14 6 1 98670 338 33 75 44 10 26 108 1 5 606 119 | Leu 29 24 9 1 7 21 8 3 3 271 99202 21 57 124 18 61 16 5 11 109 120 | Lys 34 532 191 29 1 241 247 42 15 54 42 98287 8 7 25 103 95 0 15 31 121 | Met 27 15 5 3 3 15 11 3 0 275 261 19 99169 32 8 11 67 3 13 60 122 | Phe 10 6 8 2 13 1 14 4 6 70 245 7 14 99327 4 58 15 16 141 40 123 | Pro 71 10 14 12 5 24 17 5 7 18 42 29 4 4 99544 143 27 2 6 15 124 | Ser 355 46 164 42 40 29 53 111 15 33 100 83 4 48 99 98501 222 3 31 21 125 | Thr 195 37 109 19 10 18 35 15 2 161 30 88 27 14 21 255 98862 1 4 96 126 | Trp 2 27 3 1 7 4 6 13 3 7 31 1 4 46 4 9 3 99807 21 1 127 | Tyr 8 38 59 20 25 28 13 2 94 14 37 24 9 232 8 62 7 12 99292 15 128 | Val 141 11 6 5 10 4 19 15 1 744 167 24 20 31 10 20 79 0 7 98685 129 | Pai 0.076 0.062 0.041 0.037 0.009 0.038 0.049 0.084 0.025 0.081 0.101 0.050 0.022 0.051 0.043 0.062 0.054 0.018 0.031 0.066 130 | -------------------------------------------------------------------------------- /Custom/dat/cpREV64.dat: -------------------------------------------------------------------------------- 1 | 2 | 6.5 3 | 4.5 10.6 4 | 84.3 9.5 643.2 5 | 19.5 353.7 10.9 10.7 6 | 6.1 486.3 18.0 11.6 0.1 7 | 74.5 21.5 13.0 437.4 0.1 342.6 8 | 118.1 183.9 17.4 150.3 86.8 7.1 161.9 9 | 2.8 346.6 345.3 202.4 111.8 450.1 6.2 2.2 10 | 1.5 50.6 25.6 5.6 3.4 3.6 4.3 2.5 8.4 11 | 3.9 36.9 2.4 5.9 20.3 26.1 5.1 3.4 17.3 205.0 12 | 4.2 712.1 639.2 10.1 0.1 500.5 426.6 29.3 9.2 37.9 10.8 13 | 13.4 53.5 9.9 3.8 10.5 9.5 9.6 3.8 3.6 534.9 142.8 83.6 14 | 4.3 5.0 8.7 7.5 238.0 2.4 7.7 3.1 11.0 61.0 542.3 9.4 3.8 15 | 91.2 69.0 3.5 13.4 6.5 145.6 8.1 2.6 133.9 2.1 155.8 21.2 10.5 12.6 16 | 251.1 82.9 271.4 34.8 471.9 10.7 16.4 136.7 19.2 36.2 160.3 23.9 6.2 249.4 348.6 17 | 467.5 82.5 215.5 8.0 7.4 5.4 11.6 6.3 3.8 266.2 10.7 140.2 295.2 3.6 181.2 144.8 18 | 3.4 171.8 6.1 3.5 518.6 17.0 9.1 49.0 5.7 3.3 98.8 2.3 11.1 34.1 1.1 56.3 1.5 19 | 2.2 4.3 69.9 202.9 579.1 9.4 9.1 2.1 889.2 10.8 9.6 20.1 3.4 255.9 5.6 264.3 3.3 21.7 20 | 363.2 8.4 1.6 10.3 37.8 5.1 21.6 76.0 1.1 595.0 155.8 9.2 191.9 102.2 7.7 10.1 36.8 5.0 7.2 21 | 22 | 0.061007 0.060799 0.043028 0.038515 0.011297 0.035406 0.050764 0.073749 0.024609 0.085629 0.106930 0.046704 0.023382 0.056136 0.043289 0.073994 0.052078 0.018023 0.036043 0.058620 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 25 | // end of file 26 | 27 | Zhong B, Yonezawa T, Zhong Y and Hasegawa M. 2010. The position of Gnetales among seed plants: Overcoming pitfalls of chloroplast phygenomics. MBE Advance Access published July 2,2010. 28 | 29 | -------------------------------------------------------------------------------- /Custom/dat/dayhoff-dcmut.dat: -------------------------------------------------------------------------------- 1 | 0.267828 2 | 0.984474 0.327059 3 | 1.199805 0.000000 8.931515 4 | 0.360016 0.232374 0.000000 0.000000 5 | 0.887753 2.439939 1.028509 1.348551 0.000000 6 | 1.961167 0.000000 1.493409 11.388659 0.000000 7.086022 7 | 2.386111 0.087791 1.385352 1.240981 0.107278 0.281581 0.811907 8 | 0.228116 2.383148 5.290024 0.868241 0.282729 6.011613 0.439469 0.106802 9 | 0.653416 0.632629 0.768024 0.239248 0.438074 0.180393 0.609526 0.000000 0.076981 10 | 0.406431 0.154924 0.341113 0.000000 0.000000 0.730772 0.112880 0.071514 0.443504 2.556685 11 | 0.258635 4.610124 3.148371 0.716913 0.000000 1.519078 0.830078 0.267683 0.270475 0.460857 0.180629 12 | 0.717840 0.896321 0.000000 0.000000 0.000000 1.127499 0.304803 0.170372 0.000000 3.332732 5.230115 2.411739 13 | 0.183641 0.136906 0.138503 0.000000 0.000000 0.000000 0.000000 0.153478 0.475927 1.951951 1.565160 0.000000 0.921860 14 | 2.485920 1.028313 0.419244 0.133940 0.187550 1.526188 0.507003 0.347153 0.933709 0.119152 0.316258 0.335419 0.170205 0.110506 15 | 4.051870 1.531590 4.885892 0.956097 1.598356 0.561828 0.793999 2.322243 0.353643 0.247955 0.171432 0.954557 0.619951 0.459901 2.427202 16 | 3.680365 0.265745 2.271697 0.660930 0.162366 0.525651 0.340156 0.306662 0.226333 1.900739 0.331090 1.350599 1.031534 0.136655 0.782857 5.436674 17 | 0.000000 2.001375 0.224968 0.000000 0.000000 0.000000 0.000000 0.000000 0.270564 0.000000 0.461776 0.000000 0.000000 0.762354 0.000000 0.740819 0.000000 18 | 0.244139 0.078012 0.946940 0.000000 0.953164 0.000000 0.214717 0.000000 1.265400 0.374834 0.286572 0.132142 0.000000 6.952629 0.000000 0.336289 0.417839 0.608070 19 | 2.059564 0.240368 0.158067 0.178316 0.484678 0.346983 0.367250 0.538165 0.438715 8.810038 1.745156 0.103850 2.565955 0.123606 0.485026 0.303836 1.561997 0.000000 0.279379 20 | 21 | 22 | 0.087127 0.040904 0.040432 0.046872 0.033474 0.038255 0.049530 0.088612 0.033619 0.036886 0.085357 0.080481 0.014753 0.039772 0.050680 0.069577 0.058542 0.010494 0.029916 0.064718 23 | 24 | 25 | A R N D C Q E G H I L K M F P S T W Y V 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | 29 | Dayhoff rate matrix prepared using the DCMut method* 30 | ---------------------------------------------------- 31 | 32 | The first part above indicates the symmetric 'exchangeability' parameters s_ij, 33 | where s_ij = s_ji. 34 | The second part gives the amino acid equilibrium frequencies pi_i. 35 | The net replacement rate from i to j is q_ij = pi_j*s_ij. 36 | 37 | This model is usually scaled so that the mean rate of change at 38 | equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1. You should check this 39 | scaling before using the matrix above. The PAML package will perform 40 | this scaling. 41 | 42 | // 43 | 44 | *Prepared by Carolin Kosiol and Nick Goldman, December 2003. 45 | 46 | See the following paper for more details: 47 | Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. 48 | Molecular Biology and Evolution 22:193-199. 49 | 50 | See also http://www.ebi.ac.uk/goldman/dayhoff 51 | 52 | -------------------------------------------------------------------------------- /Custom/dat/dayhoff.dat: -------------------------------------------------------------------------------- 1 | 2 | 27 3 | 98 32 4 | 120 0 905 5 | 36 23 0 0 6 | 89 246 103 134 0 7 | 198 1 148 1153 0 716 8 | 240 9 139 125 11 28 81 9 | 23 240 535 86 28 606 43 10 10 | 65 64 77 24 44 18 61 0 7 11 | 41 15 34 0 0 73 11 7 44 257 12 | 26 464 318 71 0 153 83 27 26 46 18 13 | 72 90 1 0 0 114 30 17 0 336 527 243 14 | 18 14 14 0 0 0 0 15 48 196 157 0 92 15 | 250 103 42 13 19 153 51 34 94 12 32 33 17 11 16 | 409 154 495 95 161 56 79 234 35 24 17 96 62 46 245 17 | 371 26 229 66 16 53 34 30 22 192 33 136 104 13 78 550 18 | 0 201 23 0 0 0 0 0 27 0 46 0 0 76 0 75 0 19 | 24 8 95 0 96 0 22 0 127 37 28 13 0 698 0 34 42 61 20 | 208 24 15 18 49 35 37 54 44 889 175 10 258 12 48 30 157 0 28 21 | 22 | 0.087127 0.040904 0.040432 0.046872 0.033474 0.038255 0.049530 23 | 0.088612 0.033618 0.036886 0.085357 0.080482 0.014753 0.039772 24 | 0.050680 0.069577 0.058542 0.010494 0.029916 0.064718 25 | 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | S_ij = S_ji and PI_i for the Dayhoff model, with the rate Q_ij=S_ij*PI_j 29 | The rest of the file is not used. 30 | Prepared by Z. Yang, March 1995. 31 | 32 | 33 | See the following reference for notation used here: 34 | 35 | Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and 36 | applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. 37 | 38 | 39 | ----------------------------------------------------------------------- 40 | 41 | 42 | 30 43 | 109 17 44 | 154 0 532 45 | 33 10 0 0 46 | 93 120 50 76 0 47 | 266 0 94 831 0 422 48 | 579 10 156 162 10 30 112 49 | 21 103 226 43 10 243 23 10 50 | 66 30 36 13 17 8 35 0 3 51 | 95 17 37 0 0 75 15 17 40 253 52 | 57 477 322 85 0 147 104 60 23 43 39 53 | 29 17 0 0 0 20 7 7 0 57 207 90 54 | 20 7 7 0 0 0 0 17 20 90 167 0 17 55 | 345 67 27 10 10 93 40 49 50 7 43 43 4 7 56 | 772 137 432 98 117 47 86 450 26 20 32 168 20 40 269 57 | 590 20 169 57 10 37 31 50 14 129 52 200 28 10 73 696 58 | 0 27 3 0 0 0 0 0 3 0 13 0 0 10 0 17 0 59 | 20 3 36 0 30 0 10 0 40 13 23 10 0 260 0 22 23 6 60 | 365 20 13 17 33 27 37 97 30 661 303 17 77 10 50 43 186 0 17 61 | A R N D C Q E G H I L K M F P S T W Y V 62 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 63 | 64 | Accepted point mutations (x10) Figure 80 (Dayhoff 1978) 65 | ------------------------------------------------------- 66 | 67 | A 100 /* Ala */ A 0.087 /* Ala */ 68 | R 65 /* Arg */ R 0.041 /* Arg */ 69 | N 134 /* Asn */ N 0.040 /* Asn */ 70 | D 106 /* Asp */ D 0.047 /* Asp */ 71 | C 20 /* Cys */ C 0.033 /* Cys */ 72 | Q 93 /* Gln */ Q 0.038 /* Gln */ 73 | E 102 /* Glu */ E 0.050 /* Glu */ 74 | G 49 /* Gly */ G 0.089 /* Gly */ 75 | H 66 /* His */ H 0.034 /* His */ 76 | I 96 /* Ile */ I 0.037 /* Ile */ 77 | L 40 /* Leu */ L 0.085 /* Leu */ 78 | K 56 /* Lys */ K 0.081 /* Lys */ 79 | M 94 /* Met */ M 0.015 /* Met */ 80 | F 41 /* Phe */ F 0.040 /* Phe */ 81 | P 56 /* Pro */ P 0.051 /* Pro */ 82 | S 120 /* Ser */ S 0.070 /* Ser */ 83 | T 97 /* Thr */ T 0.058 /* Thr */ 84 | W 18 /* Trp */ W 0.010 /* Trp */ 85 | Y 41 /* Tyr */ Y 0.030 /* Tyr */ 86 | V 74 /* Val */ V 0.065 /* Val */ 87 | 88 | scale factor = SUM_OF_PRODUCT = 75.246 89 | 90 | 91 | Relative Mutability The equilibrium freqs. 92 | (Table 21) Table 22 93 | (Dayhoff 1978) Dayhoff (1978) 94 | ---------------------------------------------------------------- 95 | 96 | 97 | 98 | Some notes from 1995, for those technical people: 99 | 100 | I managed to find some notes I wrote in 1995. The symbols are not 101 | that comprehensible now, but you can get the basic idea, I think. 102 | 103 | (1) Construction of P(0.01), for 1 PAM 104 | p_ij(0.01) = m_i * A_{ij}/\sum_k{A_{ik}} / 7524.6 105 | 106 | (2) Eigensolution of P(0.01) = exp{Q*0.01} 107 | P(0.01) = U diag{\lambda...} U^{-1} 108 | 109 | Then 110 | Q = U diag{100*log{\lambda}...} U^{-1} 111 | 112 | 113 | I did not use the PAM transition probabilities as rates assuming 0.01 114 | is close to 0, but instead take them as P(0.01) to recover the rate 115 | matrix, and as we expect, the rates are more different from each other 116 | than the p_ij(0.01) are. 117 | 118 | I seem to recall that I thought some details in the Dayhoff paper and 119 | the Kishino et al. (1990) paper were not entirely right. I think I 120 | thought that Q should be a symmetrical matrix, right-multiplied by a 121 | diagonal matrix, while either Dayhoff or Kishino or both used 122 | left-multiplication. 123 | 124 | As far as I know, codeml and protml give very similar (but not 125 | identical, I think) results under the Dayhoff model. 126 | 127 | My jones.dat file is not based on the Jones et al. (1992) paper, but 128 | is based on an updated data set sent to me by David Jones. So codeml 129 | and protml gave different results under JTT, but ranking of trees was 130 | not affected for the data set I tested. 131 | 132 | Ziheng Yang 133 | -------------------------------------------------------------------------------- /Custom/dat/g1974a.dat: -------------------------------------------------------------------------------- 1 | 0.189 2 | 0.026 0.215 3 | 0.175 0.364 0.149 4 | 0.074 0.263 0.048 0.101 5 | 0.043 0.146 0.069 0.218 0.117 6 | 0.136 0.325 0.110 0.039 0.062 0.179 7 | 0.037 0.152 0.063 0.212 0.111 0.006 0.173 8 | 0.430 0.241 0.456 0.605 0.504 0.387 0.566 0.393 9 | 0.111 0.078 0.137 0.286 0.185 0.068 0.247 0.074 0.319 10 | 0.102 0.087 0.128 0.277 0.176 0.059 0.238 0.065 0.328 0.009 11 | 0.159 0.030 0.185 0.334 0.233 0.116 0.295 0.122 0.271 0.048 0.057 12 | 0.069 0.120 0.095 0.244 0.143 0.026 0.205 0.032 0.361 0.042 0.033 0.090 13 | 0.548 0.359 0.574 0.723 0.622 0.505 0.684 0.511 0.118 0.437 0.446 0.389 0.479 14 | 0.094 0.095 0.120 0.269 0.168 0.051 0.230 0.057 0.336 0.017 0.008 0.065 0.025 0.454 15 | 0.043 0.232 0.017 0.132 0.031 0.086 0.093 0.080 0.473 0.154 0.145 0.202 0.112 0.591 0.137 16 | 0.098 0.287 0.072 0.077 0.024 0.141 0.038 0.135 0.528 0.209 0.200 0.257 0.167 0.646 0.192 0.055 17 | 0.603 0.414 0.629 0.778 0.677 0.560 0.739 0.566 0.173 0.492 0.501 0.444 0.534 0.055 0.509 0.646 0.701 18 | 0.491 0.302 0.517 0.666 0.565 0.448 0.627 0.454 0.061 0.380 0.389 0.332 0.422 0.057 0.397 0.534 0.589 0.112 19 | 0.045 0.234 0.019 0.130 0.029 0.088 0.091 0.082 0.475 0.156 0.147 0.204 0.114 0.593 0.139 0.002 0.053 0.648 0.536 20 | 21 | A R N D C Q E G H I L K M F P S T W Y V 22 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 23 | 24 | 25 | aromaticity ( data from Xuhua Xia): d_ij=|d_i - d_j| 26 | d_max = 0.778 27 | 28 | Prepared by Z Yang 29 | Thu Apr 1 16:19:06 BST 1999 30 | -------------------------------------------------------------------------------- /Custom/dat/g1974c.dat: -------------------------------------------------------------------------------- 1 | 2 | 0.65 3 | 1.33 0.68 4 | 1.38 0.73 0.05 5 | 2.75 2.10 1.42 1.37 6 | 0.89 0.24 0.44 0.49 1.86 7 | 0.92 0.27 0.41 0.46 1.83 0.03 8 | 0.74 0.09 0.59 0.64 2.01 0.15 0.18 9 | 0.58 0.07 0.75 0.80 2.17 0.31 0.34 0.16 10 | 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 11 | 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 12 | 0.33 0.32 1.00 1.05 2.42 0.56 0.59 0.41 0.25 0.33 0.33 13 | 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 0.00 0.33 14 | 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 0.00 0.33 0.00 15 | 0.39 0.26 0.94 0.99 2.36 0.50 0.53 0.35 0.19 0.39 0.39 0.06 0.39 0.39 16 | 1.42 0.77 0.09 0.04 1.33 0.53 0.50 0.68 0.84 1.42 1.42 1.09 1.42 1.42 1.03 17 | 0.71 0.06 0.62 0.67 2.04 0.18 0.21 0.03 0.13 0.71 0.71 0.38 0.71 0.71 0.32 0.71 18 | 0.13 0.52 1.20 1.25 2.62 0.76 0.79 0.61 0.45 0.13 0.13 0.20 0.13 0.13 0.26 1.29 0.58 19 | 0.20 0.45 1.13 1.18 2.55 0.69 0.72 0.54 0.38 0.20 0.20 0.13 0.20 0.20 0.19 1.22 0.51 0.07 20 | 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 21 | 22 | A R N D C Q E G H I L K M F P S T W Y V 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 0 .65 1.33 1.38 2.75 .89 .92 .74 .58 0 0 .33 0 0 .39 1.42 .71 .13 .20 0 25 | 26 | Composition from Grantham (1974): d_ij=|d_i - d_j| 27 | d_max = 2.75 28 | Prepared by Z Yang, 6 May 1998. 29 | -------------------------------------------------------------------------------- /Custom/dat/g1974p.dat: -------------------------------------------------------------------------------- 1 | 2 | 2.4 3 | 3.5 1.1 4 | 4.9 2.5 1.4 5 | 2.6 5.0 6.1 7.5 6 | 2.4 0.0 1.1 2.5 5.0 7 | 4.2 1.8 0.7 0.7 6.8 1.8 8 | 0.9 1.5 2.6 4.0 3.5 1.5 3.3 9 | 2.3 0.1 1.2 2.6 4.9 0.1 1.9 1.4 10 | 2.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.2 11 | 3.2 5.6 6.7 8.1 0.6 5.6 7.4 4.1 5.5 0.3 12 | 3.2 0.8 0.3 1.7 5.8 0.8 1.0 2.3 0.9 6.1 6.4 13 | 2.4 4.8 5.9 7.3 0.2 4.8 6.6 3.3 4.7 0.5 0.8 5.6 14 | 2.9 5.3 6.4 7.8 0.3 5.3 7.1 3.8 5.2 0.0 0.3 6.1 0.5 15 | 0.1 2.5 3.6 5.0 2.5 2.5 4.3 1.0 2.4 2.8 3.1 3.3 2.3 2.8 16 | 1.1 1.3 2.4 3.8 3.7 1.3 3.1 0.2 1.2 4.0 4.3 2.1 3.5 4.0 1.2 17 | 0.5 1.9 3.0 4.4 3.1 1.9 3.7 0.4 1.8 3.4 3.7 2.7 2.9 3.4 0.6 0.6 18 | 2.7 5.1 6.2 7.6 0.1 5.1 6.9 3.6 5.0 0.2 0.5 5.9 0.3 0.2 2.6 3.8 3.2 19 | 1.9 4.3 5.4 6.8 0.7 4.3 6.1 2.8 4.2 1.0 1.3 5.1 0.5 1.0 1.8 3.0 2.4 0.8 20 | 2.2 4.6 5.7 7.1 0.4 4.6 6.4 3.1 4.5 0.7 1.0 5.4 0.2 0.7 2.1 3.3 2.7 0.5 0.3 21 | 22 | A R N D C Q E G H I L K M F P S T W Y V 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9 25 | 26 | Polarity from Grantham (1974): d_ij=|d_i - d_j| 27 | d_max = 8.1 28 | Prepared by Z Yang, 6 May 1998. 29 | -------------------------------------------------------------------------------- /Custom/dat/g1974v.dat: -------------------------------------------------------------------------------- 1 | 2 | 93 3 | 25 68 4 | 23 70 2 5 | 24 69 1 1 6 | 54 39 29 31 30 7 | 52 41 27 29 28 2 8 | 28 121 53 51 52 82 80 9 | 65 28 40 42 41 11 13 93 10 | 80 13 55 57 56 26 28 108 15 11 | 80 13 55 57 56 26 28 108 15 0 12 | 88 5 63 65 64 34 36 116 23 8 8 13 | 74 19 49 51 50 20 22 102 9 6 6 14 14 | 101 8 76 78 77 47 49 129 36 21 21 13 27 15 | 1.5 91.5 23.5 21.5 22.5 52.5 50.5 29.5 63.5 78.5 78.5 86.5 72.5 99.5 16 | 1 92 24 22 23 53 51 29 64 79 79 87 73 100 0.5 17 | 30 63 5 7 6 24 22 58 35 50 50 58 44 71 28.5 29 18 | 139 46 114 116 115 85 87 167 74 59 59 51 65 38 137.5 138 109 19 | 105 12 80 82 81 51 53 133 40 25 25 17 31 4 103.5 104 75 34 20 | 53 40 28 30 29 1 1 81 12 27 27 35 21 48 51.5 52 23 86 52 21 | 22 | A R N D C Q E G H I L K M F P S T W Y V 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 31 124 56 54 55 85 83 3 96 111 111 119 105 132 32.5 32 61 170 136 84 25 | 26 | Volume from Grantham (1974): d_ij=|d_i - d_j| 27 | d_max = 167 28 | Prepared by Z Yang 6 May 1998. 29 | -------------------------------------------------------------------------------- /Custom/dat/grantham.dat: -------------------------------------------------------------------------------- 1 | 2 | 111 3 | 111 85 4 | 126 96 23 5 | 195 180 139 154 6 | 91 43 46 61 154 7 | 107 54 41 45 170 29 8 | 60 125 79 94 158 87 98 9 | 86 29 68 81 174 24 41 98 10 | 94 98 149 168 197 109 134 136 94 11 | 96 102 153 172 198 113 139 138 99 5 12 | 106 26 94 102 202 53 57 127 32 102 107 13 | 85 92 141 160 196 101 126 127 86 10 14 95 14 | 113 97 158 177 205 116 140 153 100 21 22 102 29 15 | 27 103 90 108 169 75 94 42 76 96 98 103 87 114 16 | 99 109 46 66 112 68 80 55 89 142 144 121 135 155 73 17 | 58 71 65 85 149 41 66 59 47 89 92 78 81 103 38 58 18 | 148 101 174 191 215 130 152 184 115 61 61 110 67 40 147 177 129 19 | 112 77 142 160 194 99 123 147 83 33 36 85 35 22 110 143 92 37 20 | 65 96 133 152 191 96 121 109 84 30 32 97 22 50 68 123 70 88 55 21 | 22 | A R N D C Q E G H I L K M F P S T W Y V 23 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 24 | 25 | 26 | Table 1 in Grantham (1974). 27 | 28 | c p v aromaticity (from Xuhua Xia) 29 | 30 | Ala 0 8.1 31 -0.11 31 | Arg .65 10.5 124 0.079 32 | Asn 1.33 11.6 56 -0.136 33 | Asp 1.38 13.0 54 -0.285 34 | Cys 2.75 5.5 55 -0.184 35 | Gln .89 10.5 85 -0.067 36 | Glu .92 12.3 83 -0.246 37 | Gly .74 9.0 3 -0.073 38 | His .58 10.4 96 0.32 39 | Ile 0 5.2 111 0.001 40 | Leu 0 4.9 111 -0.008 41 | Lys .33 11.3 119 0.049 42 | Met 0 5.7 105 -0.041 43 | Phe 0 5.2 132 0.438 44 | Pro .39 8.0 32.5 -0.016 45 | Ser 1.42 9.2 32 -0.153 46 | Thr .71 8.6 61 -0.208 47 | Trp .13 5.4 170 0.493 48 | Tyr .20 6.2 136 0.381 49 | Val 0 5.9 84 -0.155 50 | -------------------------------------------------------------------------------- /Custom/dat/jones-dcmut.dat: -------------------------------------------------------------------------------- 1 | 0.531678 2 | 0.557967 0.451095 3 | 0.827445 0.154899 5.549530 4 | 0.574478 1.019843 0.313311 0.105625 5 | 0.556725 3.021995 0.768834 0.521646 0.091304 6 | 1.066681 0.318483 0.578115 7.766557 0.053907 3.417706 7 | 1.740159 1.359652 0.773313 1.272434 0.546389 0.231294 1.115632 8 | 0.219970 3.210671 4.025778 1.032342 0.724998 5.684080 0.243768 0.201696 9 | 0.361684 0.239195 0.491003 0.115968 0.150559 0.078270 0.111773 0.053769 0.181788 10 | 0.310007 0.372261 0.137289 0.061486 0.164593 0.709004 0.097485 0.069492 0.540571 2.335139 11 | 0.369437 6.529255 2.529517 0.282466 0.049009 2.966732 1.731684 0.269840 0.525096 0.202562 0.146481 12 | 0.469395 0.431045 0.330720 0.190001 0.409202 0.456901 0.175084 0.130379 0.329660 4.831666 3.856906 0.624581 13 | 0.138293 0.065314 0.073481 0.032522 0.678335 0.045683 0.043829 0.050212 0.453428 0.777090 2.500294 0.024521 0.436181 14 | 1.959599 0.710489 0.121804 0.127164 0.123653 1.608126 0.191994 0.208081 1.141961 0.098580 1.060504 0.216345 0.164215 0.148483 15 | 3.887095 1.001551 5.057964 0.589268 2.155331 0.548807 0.312449 1.874296 0.743458 0.405119 0.592511 0.474478 0.285564 0.943971 2.788406 16 | 4.582565 0.650282 2.351311 0.425159 0.469823 0.523825 0.331584 0.316862 0.477355 2.553806 0.272514 0.965641 2.114728 0.138904 1.176961 4.777647 17 | 0.084329 1.257961 0.027700 0.057466 1.104181 0.172206 0.114381 0.544180 0.128193 0.134510 0.530324 0.089134 0.201334 0.537922 0.069965 0.310927 0.080556 18 | 0.139492 0.235601 0.700693 0.453952 2.114852 0.254745 0.063452 0.052500 5.848400 0.303445 0.241094 0.087904 0.189870 5.484236 0.113850 0.628608 0.201094 0.747889 19 | 2.924161 0.171995 0.164525 0.315261 0.621323 0.179771 0.465271 0.470140 0.121827 9.533943 1.761439 0.124066 3.038533 0.593478 0.211561 0.408532 1.143980 0.239697 0.165473 20 | 21 | 22 | 0.076862 0.051057 0.042546 0.051269 0.020279 0.041061 0.061820 0.074714 0.022983 0.052569 0.091111 0.059498 0.023414 0.040530 0.050532 0.068225 0.058518 0.014336 0.032303 0.066374 23 | 24 | 25 | A R N D C Q E G H I L K M F P S T W Y V 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | 29 | JTT rate matrix prepared using the DCMut method* 30 | ------------------------------------------------ 31 | 32 | The first part above indicates the symmetric 'exchangeability' parameters s_ij, 33 | where s_ij = s_ji. 34 | The second part gives the amino acid equilibrium frequencies pi_i. 35 | The net replacement rate from i to j is q_ij = pi_j*s_ij. 36 | 37 | This model is usually scaled so that the mean rate of change at 38 | equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1. You should check this 39 | scaling before using the matrix above. The PAML package will perform 40 | this scaling. 41 | 42 | // 43 | 44 | *Prepared by Carolin Kosiol and Nick Goldman, December 2003. 45 | 46 | See the following paper for more details: 47 | Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. 48 | Molecular Biology and Evolution 22:193-199. 49 | 50 | See also http://www.ebi.ac.uk/goldman/dayhoff 51 | -------------------------------------------------------------------------------- /Custom/dat/jones.dat: -------------------------------------------------------------------------------- 1 | 2 | 58 3 | 54 45 4 | 81 16 528 5 | 56 113 34 10 6 | 57 310 86 49 9 7 | 105 29 58 767 5 323 8 | 179 137 81 130 59 26 119 9 | 27 328 391 112 69 597 26 23 10 | 36 22 47 11 17 9 12 6 16 11 | 30 38 12 7 23 72 9 6 56 229 12 | 35 646 263 26 7 292 181 27 45 21 14 13 | 54 44 30 15 31 43 18 14 33 479 388 65 14 | 15 5 10 4 78 4 5 5 40 89 248 4 43 15 | 194 74 15 15 14 164 18 24 115 10 102 21 16 17 16 | 378 101 503 59 223 53 30 201 73 40 59 47 29 92 285 17 | 475 64 232 38 42 51 32 33 46 245 25 103 226 12 118 477 18 | 9 126 8 4 115 18 10 55 8 9 52 10 24 53 6 35 12 19 | 11 20 70 46 209 24 7 8 573 32 24 8 18 536 10 63 21 71 20 | 298 17 16 31 62 20 45 47 11 961 180 14 323 62 23 38 112 25 16 21 | 22 | 0.076748 0.051691 0.042645 0.051544 0.019803 0.040752 0.061830 23 | 0.073152 0.022944 0.053761 0.091904 0.058676 0.023826 0.040126 24 | 0.050901 0.068765 0.058565 0.014261 0.032102 0.066005 25 | 26 | // this is the end of the file. The rest are notes. 27 | 28 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 29 | 30 | S_ij = S_ji and PI_i for the Jones model based on the SWISSPROT 31 | Version 22 data. 32 | Rate Q_ij=S_ij*PI_j. 33 | The rest of the file is not used. 34 | Prepared by Z. Yang, March 1995. 35 | 36 | See the following reference for notation: 37 | 38 | Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and 39 | applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. 40 | 41 | ----------------------------------------------------------------------- 42 | 43 | 426 44 | 333 185 45 | 596 80 2134 46 | 159 214 54 20 47 | 332 1203 277 192 14 48 | 920 176 286 4497 11 1497 49 | 1853 954 470 907 158 144 999 50 | 88 716 704 244 58 1027 69 71 51 | 286 114 198 59 34 37 72 44 37 52 | 394 332 88 62 79 497 101 80 217 2086 53 | 294 3606 1209 148 15 1289 1210 215 115 121 140 54 | 185 100 56 34 27 78 50 47 33 1129 1567 167 55 | 84 21 33 16 115 14 23 28 69 354 1690 17 76 56 | 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 57 | 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 58 | 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 59 | 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 60 | 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 61 | 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 62 | 63 | A R N D C Q E G H I L K M F P S T W Y V 64 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 65 | 66 | Accepted point mutations (x10), similar to Figure 80 of Dayhoff et 67 | al. (1978). SwissProt version 22 data. 68 | ------------------------------------------------------------------------------ 69 | 70 | 256458 426 333 596 159 332 920 1853 88 286 394 294 185 84 1395 3664 3920 19 49 2771 71 | 426 182302 185 80 214 1203 176 954 716 114 332 3606 100 21 360 661 360 171 62 111 72 | 333 185 150772 2134 54 277 286 470 704 198 88 1209 56 33 64 2706 1069 9 178 86 73 | 596 80 2134 178390 20 192 4497 907 244 59 62 148 34 16 74 390 216 5 142 195 74 | 159 214 54 20 68120 14 11 158 58 34 79 15 27 115 27 559 91 60 246 150 75 | 332 1203 277 192 14 139546 1497 144 1027 37 497 1289 78 14 629 278 227 20 59 100 76 | 920 176 286 4497 11 1497 218432 999 69 72 101 1210 50 23 106 236 217 17 26 336 77 | 1853 954 470 907 158 144 999 255274 71 44 80 215 47 28 171 1861 266 106 34 420 78 | 88 716 704 244 58 1027 69 71 77124 37 217 115 33 69 249 214 116 5 777 32 79 | 286 114 198 59 34 37 72 44 37 191018 2086 121 1129 354 54 274 1420 13 102 6260 80 | 394 332 88 62 79 497 101 80 217 2086 319504 140 1567 1690 882 691 256 127 131 2020 81 | 294 3606 1209 148 15 1289 1210 215 115 121 140 206568 167 17 117 351 653 16 30 99 82 | 185 100 56 34 27 78 50 47 33 1129 1567 167 84670 76 36 89 579 15 25 937 83 | 84 21 33 16 115 14 23 28 69 354 1690 17 76 143088 66 468 54 56 1276 307 84 | 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 175488 1839 653 8 32 142 85 | 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 234536 3527 64 259 320 86 | 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 203636 18 73 805 87 | 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 50486 60 44 88 | 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 114728 63 89 | 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 223724 90 | 91 | Observed difference counts from pairwise comparisons, with ancestral sequences 92 | constructed by parsimony. F(t) = PI*P(t). 93 | Based on the SwissProt 22 data, kindly provided by D. Jones (Jones et al. 1992) 94 | ------------------------------------------------------------------------------- 95 | 96 | 97 | Ala 0.98754 0.00030 0.00023 0.00042 0.00011 0.00023 0.00065 0.00130 0.00006 0.00020 0.00028 0.00021 0.00013 0.00006 0.00098 0.00257 0.00275 0.00001 0.00003 0.00194 98 | Arg 0.00044 0.98974 0.00019 0.00008 0.00022 0.00125 0.00018 0.00099 0.00075 0.00012 0.00035 0.00376 0.00010 0.00002 0.00037 0.00069 0.00037 0.00018 0.00006 0.00012 99 | Asn 0.00042 0.00023 0.98720 0.00269 0.00007 0.00035 0.00036 0.00059 0.00089 0.00025 0.00011 0.00153 0.00007 0.00004 0.00008 0.00342 0.00135 0.00001 0.00022 0.00011 100 | Asp 0.00062 0.00008 0.00223 0.98954 0.00002 0.00020 0.00470 0.00095 0.00025 0.00006 0.00006 0.00015 0.00004 0.00002 0.00008 0.00041 0.00023 0.00001 0.00015 0.00020 101 | Cys 0.00043 0.00058 0.00015 0.00005 0.99432 0.00004 0.00003 0.00043 0.00016 0.00009 0.00021 0.00004 0.00007 0.00031 0.00007 0.00152 0.00025 0.00016 0.00067 0.00041 102 | Gln 0.00044 0.00159 0.00037 0.00025 0.00002 0.98955 0.00198 0.00019 0.00136 0.00005 0.00066 0.00170 0.00010 0.00002 0.00083 0.00037 0.00030 0.00003 0.00008 0.00013 103 | Glu 0.00080 0.00015 0.00025 0.00392 0.00001 0.00130 0.99055 0.00087 0.00006 0.00006 0.00009 0.00105 0.00004 0.00002 0.00009 0.00021 0.00019 0.00001 0.00002 0.00029 104 | Gly 0.00136 0.00070 0.00035 0.00067 0.00012 0.00011 0.00074 0.99350 0.00005 0.00003 0.00006 0.00016 0.00003 0.00002 0.00013 0.00137 0.00020 0.00008 0.00003 0.00031 105 | His 0.00021 0.00168 0.00165 0.00057 0.00014 0.00241 0.00016 0.00017 0.98864 0.00009 0.00051 0.00027 0.00008 0.00016 0.00058 0.00050 0.00027 0.00001 0.00182 0.00008 106 | Ile 0.00029 0.00011 0.00020 0.00006 0.00003 0.00004 0.00007 0.00004 0.00004 0.98729 0.00209 0.00012 0.00113 0.00035 0.00005 0.00027 0.00142 0.00001 0.00010 0.00627 107 | Leu 0.00023 0.00019 0.00005 0.00004 0.00005 0.00029 0.00006 0.00005 0.00013 0.00122 0.99330 0.00008 0.00092 0.00099 0.00052 0.00040 0.00015 0.00007 0.00008 0.00118 108 | Lys 0.00027 0.00331 0.00111 0.00014 0.00001 0.00118 0.00111 0.00020 0.00011 0.00011 0.00013 0.99100 0.00015 0.00002 0.00011 0.00032 0.00060 0.00001 0.00003 0.00009 109 | Met 0.00042 0.00023 0.00013 0.00008 0.00006 0.00018 0.00011 0.00011 0.00007 0.00255 0.00354 0.00038 0.98818 0.00017 0.00008 0.00020 0.00131 0.00003 0.00006 0.00212 110 | Phe 0.00011 0.00003 0.00004 0.00002 0.00015 0.00002 0.00003 0.00004 0.00009 0.00047 0.00227 0.00002 0.00010 0.99360 0.00009 0.00063 0.00007 0.00008 0.00171 0.00041 111 | Pro 0.00148 0.00038 0.00007 0.00008 0.00003 0.00067 0.00011 0.00018 0.00026 0.00006 0.00093 0.00012 0.00004 0.00007 0.99270 0.00194 0.00069 0.00001 0.00003 0.00015 112 | Ser 0.00287 0.00052 0.00212 0.00031 0.00044 0.00022 0.00018 0.00146 0.00017 0.00021 0.00054 0.00027 0.00007 0.00037 0.00144 0.98556 0.00276 0.00005 0.00020 0.00025 113 | Thr 0.00360 0.00033 0.00098 0.00020 0.00008 0.00021 0.00020 0.00024 0.00011 0.00131 0.00024 0.00060 0.00053 0.00005 0.00060 0.00324 0.98665 0.00002 0.00007 0.00074 114 | Trp 0.00007 0.00065 0.00003 0.00002 0.00023 0.00008 0.00006 0.00040 0.00002 0.00005 0.00048 0.00006 0.00006 0.00021 0.00003 0.00024 0.00007 0.99686 0.00023 0.00017 115 | Tyr 0.00008 0.00010 0.00030 0.00024 0.00041 0.00010 0.00004 0.00006 0.00130 0.00017 0.00022 0.00005 0.00004 0.00214 0.00005 0.00043 0.00012 0.00010 0.99392 0.00011 116 | Val 0.00226 0.00009 0.00007 0.00016 0.00012 0.00008 0.00027 0.00034 0.00003 0.00511 0.00165 0.00008 0.00076 0.00025 0.00012 0.00026 0.00066 0.00004 0.00005 0.98761 117 | 118 | P(0.01), amino acid exchange data generated from SWISSPROT Release 22.0 119 | Ref. Jones D.T., Taylor W.R. and Thornton J.M. (1992) CABIOS 8:275-282 120 | 121 | 122 | Usable sequences: 23824 123 | Final alignments: 5437 124 | Accepted point mutations: 92883 125 | 126 | A R N D C Q E G H I L K M F P S T W Y V 127 | 128 | 129 | 0.0767477 100 130 | 0.0516907 82.3263 131 | 0.0426448 102.697 132 | 0.0515445 83.8924 133 | 0.0198027 45.6097 134 | 0.0407523 83.8825 135 | 0.0618296 75.7914 136 | 0.0731516 52.1273 137 | 0.0229438 91.1374 138 | 0.0537609 101.99 139 | 0.0919042 53.7672 140 | 0.0586762 72.2308 141 | 0.0238262 94.8144 142 | 0.0401265 51.3146 143 | 0.0509007 58.5874 144 | 0.0687652 115.899 145 | 0.0585647 107.092 146 | 0.0142613 25.2297 147 | 0.0321015 48.7629 148 | 0.0660051 99.4571 149 | 150 | Normalized Relative 151 | frequency mutabilities 152 | (SUM m*f) = 80.240436 153 | ------------------------------------------- 154 | -------------------------------------------------------------------------------- /Custom/dat/lg.dat: -------------------------------------------------------------------------------- 1 | 0.425093 2 | 0.276818 0.751878 3 | 0.395144 0.123954 5.076149 4 | 2.489084 0.534551 0.528768 0.062556 5 | 0.969894 2.807908 1.695752 0.523386 0.084808 6 | 1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 7 | 2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 8 | 0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 9 | 0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 10 | 0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 11 | 0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 12 | 1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 13 | 0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 14 | 1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 15 | 4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 16 | 2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 17 | 0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 18 | 0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 19 | 2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 20 | 21 | 0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147 22 | 23 | A R N D C Q E G H I L K M F P S T W Y V 24 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 25 | 26 | Symmetrical part of the rate matrix and aa frequencies, 27 | estimated from 3905 globular protein amino acid sequences forming 182 28 | protein families. 29 | The first part above indicates the symmetric 'exchangeability' 30 | parameters, where s_ij = s_ji. The s_ij above are not scaled, but the 31 | PAML package will perform this scaling. 32 | The second part gives the amino acid frequencies (pi_i) 33 | estimated from the 3905 sequences. The net replacement rate from i to 34 | j is Q_ij = s_ij*pi_j. 35 | 36 | 37 | Citation: 38 | 39 | Le, S. Q., and O. Gascuel. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320. 40 | -------------------------------------------------------------------------------- /Custom/dat/miyata.dat: -------------------------------------------------------------------------------- 1 | 2 | 2.92 3 | 1.78 2.04 4 | 2.37 2.34 0.65 5 | 1.39 3.06 2.83 3.48 6 | 1.92 1.13 0.99 1.47 2.48 7 | 2.46 1.45 0.85 0.90 3.26 0.84 8 | 0.91 3.58 1.96 2.37 2.22 2.48 2.78 9 | 2.17 0.82 1.29 1.72 2.56 0.32 0.96 2.78 10 | 2.69 2.49 3.37 3.98 1.63 2.57 3.39 3.60 2.45 11 | 2.76 2.62 3.49 4.10 1.65 2.70 3.53 3.67 2.59 0.14 12 | 2.96 0.40 1.84 2.05 3.27 1.06 1.14 3.54 0.79 2.84 2.98 13 | 2.42 2.29 3.08 3.69 1.46 2.30 3.13 3.34 2.19 0.29 0.41 2.63 14 | 3.23 2.47 3.70 4.27 2.24 2.81 3.59 4.14 2.63 0.61 0.63 2.85 0.82 15 | 0.06 2.90 1.80 2.40 1.33 1.92 2.48 0.97 2.15 2.62 2.70 2.94 2.36 3.17 16 | 0.51 2.74 1.31 1.87 1.84 1.65 2.06 0.85 1.94 2.95 3.04 2.71 2.67 3.45 0.56 17 | 0.90 2.03 1.40 2.05 1.45 1.12 1.83 1.70 1.32 2.14 2.25 2.10 1.86 2.60 0.87 0.89 18 | 4.23 2.72 4.39 4.88 3.34 3.42 4.08 5.13 3.16 1.72 1.73 3.11 1.89 1.11 4.17 4.38 3.50 19 | 3.18 2.02 3.42 3.95 2.38 2.48 3.22 4.08 2.27 0.86 0.94 2.42 0.93 0.48 3.12 3.33 2.45 1.06 20 | 1.85 2.43 2.76 3.40 0.86 2.13 2.97 2.76 2.11 0.85 0.91 2.70 0.62 1.43 1.79 2.15 1.42 2.51 1.52 21 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 22 | 23 | 24 | Dmin: 0.06 Pro-Ala 25 | Dmax: 5.13 Trp-Gly 26 | 27 | Miyata, T., S. Miyazawa, and T. Yasunaga. 1979. Two types of amino 28 | acid substitutions in protein evolution. J. Mol. Evol. 12:219-236. 29 | -------------------------------------------------------------------------------- /Custom/dat/mtArt.dat: -------------------------------------------------------------------------------- 1 | 2 | 0.2 3 | 0.2 0.2 4 | 1 4 500 5 | 254 36 98 11 6 | 0.2 154 262 0.2 0.2 7 | 0.2 0.2 183 862 0.2 262 8 | 200 0.2 121 12 81 3 44 9 | 0.2 41 180 0.2 12 314 15 0.2 10 | 26 2 21 7 63 11 7 3 0.2 11 | 4 2 13 1 79 16 2 1 6 515 12 | 0.2 209 467 2 0.2 349 106 0.2 0.2 3 4 13 | 121 5 79 0.2 312 67 0.2 56 0.2 515 885 106 14 | 13 5 20 0.2 184 0.2 0.2 1 14 118 263 11 322 15 | 49 0.2 17 0.2 0.2 39 8 0.2 1 0.2 12 17 5 15 16 | 673 3 398 44 664 52 31 226 11 7 8 144 112 36 87 17 | 244 0.2 166 0.2 183 44 43 0.2 19 204 48 70 289 14 47 660 18 | 0.2 0.2 8 0.2 22 7 11 2 0.2 0.2 21 16 71 54 0.2 2 0.2 19 | 1 4 251 0.2 72 87 8 9 191 12 20 117 71 792 18 30 46 38 20 | 340 0.2 23 0.2 350 0.2 14 3 0.2 1855 85 26 281 52 32 61 544 0.2 2 21 | 22 | 0.054116 0.018227 0.039903 0.020160 0.009709 0.018781 0.024289 0.068183 0.024518 0.092638 23 | 0.148658 0.021718 0.061453 0.088668 0.041826 0.091030 0.049194 0.029786 0.039443 0.057700 24 | 25 | 26 | 27 | // this is the end of the file. The rest are notes. 28 | 29 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 30 | 31 | This model has been derived from 36 artropoda mitochondrial genomes. 32 | 33 | Each gene of the given species was aligned individually. Then, alignments of the whole set 34 | of 13 genes where concatenated and passed through GBlocks (Castresana, 2000, in JME) with 35 | parameters and output: 36 | 37 | Minimum Number Of Sequences For A Conserved Position: 20 38 | Minimum Number Of Sequences For A Flanking Position: 32 39 | Maximum Number Of Contiguous Nonconserved Positions: 8 40 | Minimum Length Of A Block: 10 41 | Allowed Gap Positions: With Half 42 | Use Similarity Matrices: Yes 43 | 44 | Flank positions of the 40 selected block(s) 45 | Flanks: [6 22] [26 44] [61 70] [77 143] [145 185] [208 236] [309 640] 46 | [644 802] [831 941] [956 966] [973 1062] [1085 1339] [1343 1702] 47 | [1754 1831] [1840 1911] [1916 1987] [2011 2038] [2097 2118] [2125 2143] 48 | [2179 2215] [2243 2268] [2277 2288] [2333 2347] [2476 2518] [2539 2558] 49 | [2600 2613] [2637 2672] [2738 2759] [2784 2839] [2882 2924] [2948 3097] 50 | [3113 3123] [3210 3235] [3239 3322] [3348 3392] [3406 3526] [3588 3617] 51 | [3660 3692] [3803 3830] [3909 3928] 52 | 53 | New number of positions in MtArt-strict.phy.fasta-gb: 2664 (67% of the original 3933 positions) 54 | 55 | The species included in the analysis were: 56 | Harpiosquilla harpax [NCBI_TaxID 287944] 57 | Ixodes uriae [NCBI_TaxID 59655] 58 | Heptathela hangzhouensis [NCBI_TaxID 216259] 59 | Triops longicaudatus [NCBI_TaxID 58777] 60 | Gryllotalpa orientalis [NCBI_TaxID 213494] 61 | lepidopsocid RS-2001 [NCBI_TaxID 159971] 62 | Locusta migratoria [NCBI_TaxID 7004] 63 | Drosophila yakuba [NCBI_TaxID 7245] 64 | Ostrinia furnacalis [NCBI_TaxID 93504] 65 | Megabalanus volcano [NCBI_TaxID 266495] 66 | Periplaneta fuliginosa [NCBI_TaxID 36977] 67 | Thermobia domestica [NCBI_TaxID 89055] 68 | Aleurochiton aceris [NCBI_TaxID 266942] 69 | Schizaphis graminum [NCBI_TaxID 13262] 70 | Pteronarcys princeps [NCBI_TaxID 285953] 71 | Aleurodicus dugesii [NCBI_TaxID 30099] 72 | Pollicipes polymerus [NCBI_TaxID 36137] 73 | Gomphiocephalus hodgsoni [NCBI_TaxID 221270] 74 | Habronattus oregonensis [NCBI_TaxID 130930] 75 | Speleonectes tulumensis [NCBI_TaxID 84346] 76 | Hutchinsoniella macracantha [NCBI_TaxID 84335] 77 | Haemaphysalis flava [NCBI_TaxID 181088] 78 | Scutigera coleoptrata [NCBI_TaxID 29022] 79 | Vargula hilgendorfii [NCBI_TaxID 6674] 80 | Tricholepidion gertschi [NCBI_TaxID 89825] 81 | Varroa destructor [NCBI_TaxID 109461] 82 | Bombyx mandarina [NCBI_TaxID 7092] 83 | Thyropygus sp. [NCBI_TaxID 174155] 84 | Tribolium castaneum [NCBI_TaxID 7070] 85 | Pagurus longicarpus [NCBI_TaxID 111067] 86 | Limulus polyphemus [NCBI_TaxID 6850] 87 | Tetrodontophora bielanensis [NCBI_TaxID 48717] 88 | Penaeus monodon [NCBI_TaxID 6687] 89 | Daphnia pulex [NCBI_TaxID 6669] 90 | Apis mellifera [NCBI_TaxID 7469] 91 | Anopheles gambiae [NCBI_TaxID 7165] 92 | 93 | The topology used for inferring the model was: 94 | 95 | (((Daph_pulex,Trio_longi),((((((Aleu_aceri,Aleu_duges),Schi_grami),lepi_RS_20), 96 | ((((Ostr_furna,Bomb_manda),(Dros_yakub,Anop_gambi)),Apis_melli),Trib_casta)), 97 | ((Gryl_orien,Locu_migra),(Pter_princ,Peri_fulig))),(Tric_gerts,Ther_domes)), 98 | (Scut_coleo,Thyr_sp),Varg_hilge,Hutc_macra,((((Ixod_uriae,Haem_flava),Varr_destr), 99 | (Habr_orego,Hept_hangz)),Limu_polyp),(Poll_polym,Mega_volca),(Gomp_hodgs,Tetr_biela), 100 | ((Pagu_longi,Pena_monod),Harp_harpa),Spel_tulum)); 101 | 102 | Note this is not the ML topology but the consensus one (based on morphological data, 103 | phylogenetic reconstruction using nuclear genes, etc). Where relationships are 104 | not clear, a polytomy was introduced (it contains quite a lot of polytomies!). 105 | 106 | The model was estimated using Ziheng Yang's Paml software package. 107 | A four-categorized gamma distribution was used to account for heterogeneity (alpha 108 | was estimated to be 0.47821). Sites with ambiguity data were taken into account. 109 | 110 | 111 | Reference 112 | 113 | Abascal, F., D. Posada, and R. Zardoya. 2007. MtArt: A new Model of 114 | amino acid replacement for Arthropoda. Mol. Biol. Evol. 24:1-5. 115 | -------------------------------------------------------------------------------- /Custom/dat/mtREV24.dat: -------------------------------------------------------------------------------- 1 | 2 | 23.18 3 | 26.95 13.24 4 | 17.67 1.90 794.38 5 | 59.93 103.33 58.94 1.90 6 | 1.90 220.99 173.56 55.28 75.24 7 | 9.77 1.90 63.05 583.55 1.90 313.56 8 | 120.71 23.03 53.30 56.77 30.71 6.75 28.28 9 | 13.90 165.23 496.13 113.99 141.49 582.40 49.12 1.90 10 | 96.49 1.90 27.10 4.34 62.73 8.34 3.31 5.98 12.26 11 | 25.46 15.58 15.16 1.90 25.65 39.70 1.90 2.41 11.49 329.09 12 | 8.36 141.40 608.70 2.31 1.90 465.58 313.86 22.73 127.67 19.57 14.88 13 | 141.88 1.90 65.41 1.90 6.18 47.37 1.90 1.90 11.97 517.98 537.53 91.37 14 | 6.37 4.69 15.20 4.98 70.80 19.11 2.67 1.90 48.16 84.67 216.06 6.44 90.82 15 | 54.31 23.64 73.31 13.43 31.26 137.29 12.83 1.90 60.97 20.63 40.10 50.10 18.84 17.31 16 | 387.86 6.04 494.39 69.02 277.05 54.11 54.71 125.93 77.46 47.70 73.61 105.79 111.16 64.29 169.90 17 | 480.72 2.08 238.46 28.01 179.97 94.93 14.82 11.17 44.78 368.43 126.40 136.33 528.17 33.85 128.22 597.21 18 | 1.90 21.95 10.68 19.86 33.60 1.90 1.90 10.92 7.08 1.90 32.44 24.00 21.71 7.84 4.21 38.58 9.99 19 | 6.48 1.90 191.36 21.21 254.77 38.82 13.12 3.21 670.14 25.01 44.15 51.17 39.96 465.58 16.21 64.92 38.73 26.25 20 | 195.06 7.64 1.90 1.90 1.90 19.00 21.14 2.53 1.90 1222.94 91.67 1.90 387.54 6.35 8.23 1.90 204.54 5.37 1.90 21 | 22 | 23 | 0.072 0.019 0.039 0.019 0.006 0.025 0.024 0.056 0.028 0.088 0.169 24 | 0.023 0.054 0.061 0.054 0.072 0.086 0.029 0.033 0.043 25 | 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | 29 | S_ij = S_ji and PI_i for the mtREV24 model (Adachi and Hasegawa 1996). 30 | The PI's used to sum to 0.999 and I changed one of the freq from 0.168 31 | into 0.169 so that the sum is 1. Prepared by Z. Yang according to 32 | data sent by Dr M. Hasegawa. This matrix was obtained from the 12 33 | mitochondrial proteins encoded by the same strand of the DNA from a 34 | diverse range of species including bird, fish, frog, lamprey, as well 35 | as mammals (see Adachi and Hasegawa 1996 for details). The other 36 | matrix (mtmam.dat) included in the package is based on the same 37 | proteins from mammals only. 38 | 39 | Adachi, J. and Hasegawa, M. (1996) MOLPHY version 2.3: programs for 40 | molecular phylogenetics based on maximum likelihood. Computer Science 41 | Monographs of Institute of Statistical Mathematics 28:1-150. 42 | -------------------------------------------------------------------------------- /Custom/dat/mtmam.dat: -------------------------------------------------------------------------------- 1 | 32 2 | 2 4 3 | 11 0 864 4 | 0 186 0 0 5 | 0 246 8 49 0 6 | 0 0 0 569 0 274 7 | 78 18 47 79 0 0 22 8 | 8 232 458 11 305 550 22 0 9 | 75 0 19 0 41 0 0 0 0 10 | 21 6 0 0 27 20 0 0 26 232 11 | 0 50 408 0 0 242 215 0 0 6 4 12 | 76 0 21 0 0 22 0 0 0 378 609 59 13 | 0 0 6 5 7 0 0 0 0 57 246 0 11 14 | 53 9 33 2 0 51 0 0 53 5 43 18 0 17 15 | 342 3 446 16 347 30 21 112 20 0 74 65 47 90 202 16 | 681 0 110 0 114 0 4 0 1 360 34 50 691 8 78 614 17 | 5 16 6 0 65 0 0 0 0 0 12 0 13 0 7 17 0 18 | 0 0 156 0 530 54 0 1 1525 16 25 67 0 682 8 107 0 14 19 | 398 0 0 10 0 33 20 5 0 2220 100 0 832 6 0 0 237 0 0 20 | 21 | 22 | 0.0692 0.0184 0.0400 0.0186 0.0065 0.0238 0.0236 0.0557 0.0277 0.0905 23 | 0.1675 0.0221 0.0561 0.0611 0.0536 0.0725 0.0870 0.0293 0.0340 0.0428 24 | 25 | A R N D C Q E G H I L K M F P S T W Y V 26 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 27 | 28 | //End of File 29 | 30 | 31 | Symmetrical part of the rate matrix and aa frequencies, estimated from 32 | the 12 mt proteins (atp6 atp8 cox1 cox2 cox3 cytb nd1 nd2 nd3 nd4 nd4l 33 | nd5) on the same strand of the mitochondrial DNA (3331 sites). The 34 | data are from 20 species of mammals and three close outgroups 35 | (wallaroo, opossum, and platypus). The model used is 36 | REVaa+dGamma(K=8) with the estimated gamma parameter to be 0.37. The 37 | first part is S_ij = S_ji, and the second part has the amino acid 38 | frequencies (PI_i). The substitution rate from amino acid i to j is 39 | Q_ij=S_ij*PI_j. 40 | 41 | 42 | The data are from 43 | 44 | Cao, Y. et al. 1998 Conflict amongst individual mitochondrial proteins 45 | in resolving the phylogeny of eutherian orders. Journal of 46 | Molecular Evolution 15:1600-1611. 47 | 48 | The species are listed below 49 | 50 | 1 SB17F Homo sapiens (African) # D38112 51 | 2 CHIMP Pan troglodytes (chimpanzee) # D38113 52 | 3 PyGC Pan paniscus (bonobo) # D38116 53 | 4 GORIL Gorilla gorilla (gorilla) # D38114 54 | 5 ORANG Pongo pygmaeus (orangutan) # D38115 55 | 6 Ponpy Pongo pygmaeus abelii (Sumatran orangutan) # X97707 56 | 7 Hylla Hylobates lar (common gibbon) # X99256 (lar gibbon) 57 | 8 Phovi Phoca vitulina (harbor seal) # X63726 58 | 9 Halgr Halichoerus grypus (grey seal) # X72004 59 | 10 Felca Felis catus (cat) # U20753 60 | 11 Equca Equus caballus (horse) # X79547 61 | 12 Rhiun Rhinoceros unicornis (Indian rhinoceros) # X97336 62 | 13 Bosta Bos taurus (cow) # J01394 63 | 14 Balph Balaenoptera physalus (fin whale) # X61145 64 | 15 Balmu Balaenoptera musculus (blue whale) # X72204 65 | 16 Ratno Rattus norvegicus (rat) # X14848 66 | 17 Musmu Mus musculus (mouse) # J01420 67 | 18 Macro Macropus robustus (wallaroo) # Y10524 68 | 19 Didvi Didelphis virginiana (opossum) # Z29573 69 | 20 Ornan Ornithorhynchus anatinus (platypus) # X83427 70 | 71 | 72 | The results and details of the model are published in 73 | 74 | Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid 75 | substitution and applications to Mitochondrial protein evolution, 76 | Molecular Biology and Evolution 15:1600-1611. 77 | 78 | Prepared by Z. Yang, April 1998. 79 | -------------------------------------------------------------------------------- /Custom/dat/wag.dat: -------------------------------------------------------------------------------- 1 | 0.551571 2 | 0.509848 0.635346 3 | 0.738998 0.147304 5.429420 4 | 1.027040 0.528191 0.265256 0.0302949 5 | 0.908598 3.035500 1.543640 0.616783 0.0988179 6 | 1.582850 0.439157 0.947198 6.174160 0.021352 5.469470 7 | 1.416720 0.584665 1.125560 0.865584 0.306674 0.330052 0.567717 8 | 0.316954 2.137150 3.956290 0.930676 0.248972 4.294110 0.570025 0.249410 9 | 0.193335 0.186979 0.554236 0.039437 0.170135 0.113917 0.127395 0.0304501 0.138190 10 | 0.397915 0.497671 0.131528 0.0848047 0.384287 0.869489 0.154263 0.0613037 0.499462 3.170970 11 | 0.906265 5.351420 3.012010 0.479855 0.0740339 3.894900 2.584430 0.373558 0.890432 0.323832 0.257555 12 | 0.893496 0.683162 0.198221 0.103754 0.390482 1.545260 0.315124 0.174100 0.404141 4.257460 4.854020 0.934276 13 | 0.210494 0.102711 0.0961621 0.0467304 0.398020 0.0999208 0.0811339 0.049931 0.679371 1.059470 2.115170 0.088836 1.190630 14 | 1.438550 0.679489 0.195081 0.423984 0.109404 0.933372 0.682355 0.243570 0.696198 0.0999288 0.415844 0.556896 0.171329 0.161444 15 | 3.370790 1.224190 3.974230 1.071760 1.407660 1.028870 0.704939 1.341820 0.740169 0.319440 0.344739 0.967130 0.493905 0.545931 1.613280 16 | 2.121110 0.554413 2.030060 0.374866 0.512984 0.857928 0.822765 0.225833 0.473307 1.458160 0.326622 1.386980 1.516120 0.171903 0.795384 4.378020 17 | 0.113133 1.163920 0.0719167 0.129767 0.717070 0.215737 0.156557 0.336983 0.262569 0.212483 0.665309 0.137505 0.515706 1.529640 0.139405 0.523742 0.110864 18 | 0.240735 0.381533 1.086000 0.325711 0.543833 0.227710 0.196303 0.103604 3.873440 0.420170 0.398618 0.133264 0.428437 6.454280 0.216046 0.786993 0.291148 2.485390 19 | 2.006010 0.251849 0.196246 0.152335 1.002140 0.301281 0.588731 0.187247 0.118358 7.821300 1.800340 0.305434 2.058450 0.649892 0.314887 0.232739 1.388230 0.365369 0.314730 20 | 21 | 0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 22 | 23 | 24 | // this is the end of the file. The rest are notes. 25 | 26 | 27 | A R N D C Q E G H I L K M F P S T W Y V 28 | Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 29 | 30 | Symmetrical part of the rate matrix and aa frequencies, 31 | estimated from 3905 globular protein amino acid sequences forming 182 32 | protein families. 33 | The first part above indicates the symmetric 'exchangeability' 34 | parameters, where s_ij = s_ji. The s_ij above are not scaled, but the 35 | PAML package will perform this scaling. 36 | The second part gives the amino acid frequencies (pi_i) 37 | estimated from the 3905 sequences. The net replacement rate from i to 38 | j is Q_ij = s_ij*pi_j. 39 | Prepared by Simon Whelan and Nick Goldman, September 2000. 40 | 41 | Citation: 42 | Whelan, S. and N. Goldman. 2001. A general empirical model of 43 | protein evolution derived from multiple protein families using 44 | a maximum likelihood approach. Molecular Biology and 45 | Evolution 18, 691-699. 46 | 47 | See the following reference for notation used here: 48 | 49 | Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and 50 | applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. 51 | -------------------------------------------------------------------------------- /Custom/default.ctl: -------------------------------------------------------------------------------- 1 | seqfile = * sequence data file name 2 | treefile = * tree structure file name 3 | outfile = * main result file name 4 | 5 | noisy = 3 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 0 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 * 0:equal, +:geometric; -:linear, {1-5:G1974,Miyata,c,p,v} 14 | model = 0 15 | 16 | NSsites = 0 1 2 *（注：可以单选，也可以多选） 17 | * 0:one w; 1:NearlyNeutral; 2:PositiveSelection; 3:discrete; 18 | * 4:freqs; 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ10:3normal 19 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 20 | Mgene = 0 * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all 21 | 22 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 23 | kappa = .3 * initial or fixed kappa 24 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 25 | omega = 1.3 * initial or fixed omega, for codons or codon-based AAs 26 | ncatG = 10 * # of categories in the dG or AdG models of rates 27 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 28 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 29 | Malpha = 0 * different alphas for genes 30 | 31 | aaRatefile = dat/jones.dat 32 | ndata = 1 * 33 | 34 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 35 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 36 | 37 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 38 | method = 0 * 0: simultaneous; 1: one branch at a time 39 | Small_Diff = .45e-6 40 | cleandata = 1 -------------------------------------------------------------------------------- /Debug_Mac.sh: -------------------------------------------------------------------------------- 1 | java -jar EasyCodeML.jar 2 | -------------------------------------------------------------------------------- /Debug_Win.bat: -------------------------------------------------------------------------------- 1 | java -jar EasyCodeML.jar 2 | -------------------------------------------------------------------------------- /EasyCodeML.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/EasyCodeML.jar -------------------------------------------------------------------------------- /Example/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Example/.DS_Store -------------------------------------------------------------------------------- /Example/Example1.pml: -------------------------------------------------------------------------------- 1 | 15 483 2 | 3 | Human_ECP 4 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGCAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCGGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCACGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACCATC 5 | Goril_ECP 6 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCTTCATAACAGAACTCTCAACAATTGTCATCGGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CAGGATTCTCCACGGTATCCTGTGGTTCCTGTTCACCTGGATACCACCATC 7 | Chimp_ECP 8 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCAGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATGCCACCATC 9 | Orang_ECP 10 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTAGTGGTGTGGGGGGCTCACTCCATGCCAAACCCCGACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACGTCAGTCTGAACCCTCCTCAATGCACCACTGCAATGCGGGTAATTAACAATTATCAACGGCGTTGCAAAGACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATAACCTGTCCTCGTAACAGAACTCTCCACAATTGTCATCGGAGTAGATTCCAGGTGCCTTTACTCCACTGTAACCTCACAAATCCAGGTGCACAGAATATTTCAAACTGCAAGTATGCAGACAGAACAGAAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACCATC 11 | Macaq_ECP 12 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACAAAGGCTCAGTGGTTTGCCATCCAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTATCAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCATATACAGCTAATGTTTGTCGTAACGAACGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGTAGTAGATACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGCAGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCACCATC 13 | Macaq2_ECP 14 | ATGGTTCCAAAACTGTTCACTCCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAAGGCTCAGTGGTTTGCCATCCAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTATCAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCAAATACAGTTAATGTTTGTCGTAACCGAAGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGTAGTAGCTACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGCAGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCATCATC 15 | Orang_EDN 16 | ATGGTTCCAAAACTGTTCACTTCTCAAATTTCCCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGACGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCAACAATGCAATGCAGGTCATTAACAATTTTCAACGGCGTTGCAAAAACCAAAATACTTTTCTGCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATAACCTGTCCTAGTAACAGAAGTCGCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGGGATCCACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 17 | Chimp_EDN 18 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCAGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCATCACAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATCATC 19 | Gorilla_EDN 20 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACATCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTTGCAAAAATTGTCATCAAAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 21 | Human_EDN 22 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCACCACAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGAGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 23 | Hylobates_EDN 24 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAAACCCCAACAGTTTACCTGGGCTCAGTGGTTTGAAATCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTTCTTCGTACCACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATGACATGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAAAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCGGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCAGTAGTTCCGGTTCACCTGGATAGAATCATC 25 | Macaq_EDN 26 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATCATC 27 | Macaq2_EDN 28 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCAGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTCATC 29 | Papio_EDN 30 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTCATC 31 | Cercopith_EDN 32 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCAAAAT---ATTTCAAATTGCAAGTATACACAGACAACAGCAAACAAGTTCTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAGTCATC -------------------------------------------------------------------------------- /Example/Example1.tree: -------------------------------------------------------------------------------- 1 | (((Hylobates_EDN ,(Orang_EDN ,(Gorilla_EDN ,(Chimp_EDN ,Human_EDN )))),(Macaq_EDN ,(Cercopith_EDN ,(Macaq2_EDN ,Papio_EDN )))),(Orang_ECP,((Macaq_ECP,Macaq2_ECP),(Goril_ECP,Chimp_ECP,Human_ECP)))); 2 | 3 | -------------------------------------------------------------------------------- /Example/Example2.pml: -------------------------------------------------------------------------------- 1 | 6 1128 2 | AF335467 3 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCACUGCUGGUAGCGGGCGCAGCAAAUGCGGCUGAAAUUUAUAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCGACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCAUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUCGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGGCGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGUGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUGAGCGGCGAAGAUCAGACCAACAACGGUCGUGACUUCCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUAACUUAUGAUAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGACGAGCAGAACAAC---UCUACCUUCGUGUCUAAGACCGAUGGUGGUCGUUACGGUGUUCUGGGUGAAGGCGAUCACGCUGAAACCUACACCGGUGGUCUGAAAUACGACGCCAACAACAUCUACCUGGCGACUCAGUACACCCAGACUUACAACGCAACCCGCACCGGUAACAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUCGUUGCUCAGUACCAGUUCGACUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACCUACUACUUCAACAAAAACAUGUCCACCUACGUUGAUUACAAAAUCAACCUGCUGGACGACAACAAGUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 4 | AF336095 5 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCACUGCUGGUAGCGGGCGCAGCAAAUGCGGCUGAAAUUUAUAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCGACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCGUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUCGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGAUGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGCGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUGAGCGGCGAAGAUCAGACCAACAACGGUCGCGGCUUCCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUGACUUAUGAGAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGAUGAGCAGAACAAC---UCUACUUAUUUUUCUAAGUCCUAUCAGCGUACAUACGGUGUUCUGGGUGAAGGCGAUCACGCUGAAACCUAUACCGGUGGUCUGAAAUAUGACGCCAACAACAUUUACCUGGCGACUCAGUACACCCAGACCUACAACGCAACUCGCACUGGCGACAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUGGUUGCUCAGUACCAGUUCGACUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACCUACUACUUCAACAAAAACAUGUCCACCUACGUUGAUUACAAAAUCAACCUGCUGGACGACAACAAGUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 6 | AF336096 7 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCACUGCAGGUAGCGGGCGCAGCAUAUGCGGCUGAAAUUUAUAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCGACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCAUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUCGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGGUGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGUGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUAAGCGGCGAAGAUCAGACCAACAACGGUCGCGGCUACCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUGACUUAUGAUAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGAUGAGCAGAACAGCGUUAACACUCGUUAUACUGACUCCAACGGUGUUUCCCGUCGCGUACUGGGUGAAGGCGAUCACGCUGAAACCUACACCGGUGGUCUGAAAUACGACGCCAACAACAUCUACCUGGCGACUCAGUACACCCAGACCUACAACGCAACCCGCACCGGUAUCAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUAGUUGCUCAGUACCAGUUCGACUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACUUACUACUUCAACAAAAACGUGUCCACGUACGUUGAUUACAAAAUCAACCUGCUGGACGACAACUGUUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 8 | AF336097 9 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCACUGCUGGUAGCGGGCGCAGCAAAUGCGGCUGAAAUCUACAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCGACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCGUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUCGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGGUGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGCGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUGAGCGGCGAAGAUCAGACCAACAACGGUCGCGGCUUCCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUGACUUAUGAGAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGAUGAGCAGAACAAC---UCUACUUAUUUUUCUAAGUCCUAUCAGCGUACAUACGGUGUUCUGGGUGAAGGCGAUCACGCUGAAACCUAUACCGGUGGUCUGAAAUAUGACGCCAACAACAUUUACCUGGCGACUCAGUACACCCAGACCUACAACGCAACUCGCACUGGCGACAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUGGUUGCUCAGUACCAGUUCGACUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACCUACUACUUCAACAAAAACAUGUCCACCUACGUUGAUUACAAAAUCAACCUGCUGGACGACAACAAGUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 10 | AF336098 11 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCACUGCUGGUAGCGGGCGCAGCAAAUGCGGCUGAAAUUUAUAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCUACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCGUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUCGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGAUGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGUGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUGAGCGGCGAAGAUCAGACCAACAACGGUCGCGGCUUCCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUGACUUAUGAGAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGAUGAGCAGAACAAC---UCUACUUACUUUUCUAAGUCCUAUCGUCGUACAUACGGUGUUCUGGGUGAAGGCGAUCACGCUGAAACCUAUACCGGUGGUCUGAAAUAUGACGCCAACAACAUUUACCUGGCGACUCAGUACACCCAGACCUACAACGCAACUCGCACUGGCGACAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUGGUUGCUCAGUACCAGUUCGACUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACCUACUACUUCAACAAAAACAUGUCCACCUACGUUGAUUACAAAAUCAACCUGCUGGACGACAACAAGUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 12 | AF373860 13 | AUGAAAGUUAAAGUACUGUCCCUCCUGGUACCAGCUCUGCUGGUAGCGGGCGCAGCAAAUGCGGCUGAAAUUUAUAACAAAGACGGCAACAAAUUAGACCUGUACGGUAAAAUCGACGGUCUGCACUACUUCUCUUCCGACGACAGCGUCGACGGCGACCAGACCUACAUGCGUAUCGGCGUGAAAGGCGAAACCCAGAUCAACGACCAGCUGACCGGUUACGGCCAGUGGGAAUACAACGUUCAGGCGAACAACACUGAAAGCUCCAGCGACCAGGCGUGGACUCGUCUGGCCUUCGCGGGUCUGAAAUUAGGCGACGCGGGUUCUUUCGACUACGGUCGUAACUACGGCGUUGUUUACGACGUAACUUCCUGGACCGACGUUCUGCCGGAAUUCGGUGGCGACACCUACGGUUCCGACAACUUCCUGCAGUCCCGUGCUAACGGCGUUGCCACCUACCGUAACUCUGACUUCUUCGGUCUGGUUGACGGCCUGAACUUUGCUCUGCAGUACCAGGGUAAAAACGGCAGCGUGAGCGGCGAAGAUCAGACCAACAACGGUCGCGGCUUCCAGAAACAGAACGGCGAAGGCUUCGGCACCUCCGUGACUUAUGAGAUCUGGGACGGCAUCAGCGCUGGUUUCGCGUACUCCAGCUCUAAACGUACCGAUGAGCAGAACAAC---UCUACUUAUUUUUCUAAGUCCUAUCAGCGUACAUACGGUGUUCUGGGUGAAGGCGAUCACGCUGAAACCUAUACCGGUGGUCUGAAAUAUGACGCCAACAACAUUUACCUGGCGACUCAGUACACCCAGACCUACAACGCAACUCGCACUGGCGACAUCGGUUUUGCUAACAAAGCGCAGAACUUCGAAGUGGUUGCUCAGUACCAGUUCGAUUUCGGUCUGCGUCCGUCCGUGGCUUACCUGCAGUCUAAAGGUAAAGACAUGGGCCGUUACGGCGACCAGGACAUCCUGAAAUAUGUUGACCUGGGUGCGACCUACUACUUCAACAAAAACAUGUCCACCUACGUUGAUUACAAAAUCCACCUGCUGGACGACAACAAGUUCACUAAAGAUGCAAGCAUCUCUACUGACAACGUUGUGGCUCUGGGCCUGGUUUACCAGUUC 14 | -------------------------------------------------------------------------------- /Example/Example2.tre: -------------------------------------------------------------------------------- 1 | ((((AF336097:0.0018008106,AF373860:0.0036487888):8.83E-4,AF336095:2.6178E-6):0.003549,AF336098:9.636206E-4):0.015002,AF335467:0.0134404779,AF336096:0.0352820318); -------------------------------------------------------------------------------- /Preset/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/.DS_Store -------------------------------------------------------------------------------- /Preset/BM/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BM/.DS_Store -------------------------------------------------------------------------------- /Preset/BM/BM/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BM/BM/.DS_Store -------------------------------------------------------------------------------- /Preset/BM/BM/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = ArMV.nuc 2 | treefile = ArMV.trees 3 | outfile = mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 2 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 0 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/BM/FR/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BM/FR/.DS_Store -------------------------------------------------------------------------------- /Preset/BM/FR/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = Seq_ATP1A1.txt 2 | treefile = ATP1A1.trees 3 | outfile = FM_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 1 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted 13 | aaDist = 0 14 | model = 1 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive 19 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 20 | 21 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 22 | kappa = 2 * initial or fixed kappa 23 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 24 | omega = 1 * initial or fixed omega, for codons or codon-transltd AAs 25 | 26 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 27 | alpha = 0 * initial or fixed alpha, 0:infinity (constant rate) 28 | Malpha = 0 * different alphas for genes 29 | ncatG = 4 * # of categories in the dG or AdG models of rates 30 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 31 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 32 | method = 0 * 0: simultaneous; 1: one branch at a time 33 | Small_Diff = .45e-6 34 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 35 | 36 | 37 | * Free-ratio model 38 | -------------------------------------------------------------------------------- /Preset/BM/M0/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BM/M0/.DS_Store -------------------------------------------------------------------------------- /Preset/BM/M0/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = 36.nuc 2 | treefile = 36ML.trees 3 | outfile = M0_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 0 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/BSM/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BSM/.DS_Store -------------------------------------------------------------------------------- /Preset/BSM/ModelA/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = 36.nuc 2 | treefile = 36ML.trees 3 | outfile = A_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 2 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 2 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/BSM/ModelAnull/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/BSM/ModelAnull/.DS_Store -------------------------------------------------------------------------------- /Preset/BSM/ModelAnull/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = 36.nuc 2 | treefile = 36ML.trees 3 | outfile = Anull_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 2 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 2 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 1 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 1 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/CM/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/CM/.DS_Store -------------------------------------------------------------------------------- /Preset/CM/CmC/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = cmc.nuc * sequence data filename 2 | treefile = cmc.tree * tree structure file name 3 | outfile = CmC_mlc * main result file name 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 1 * 0: concise; 1: detailed, 2: too much 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | 13 | * ndata = 10 14 | clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis 15 | aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a 16 | aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) 17 | * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own 18 | 19 | model = 3 20 | * models for codons: 21 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 22 | * models for AAs or codon-translated AAs: 23 | * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F 24 | * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189) 25 | 26 | NSsites = 2 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; 27 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 28 | * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; 29 | * 13:3normal>0 30 | 31 | icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below 32 | Mgene = 0 33 | * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff 34 | * AA: 0:rates, 1:separate 35 | 36 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 37 | kappa = 3 * initial or fixed kappa 38 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 39 | omega = 1 * initial or fixed omega, for codons or codon-based AAs 40 | 41 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 42 | alpha = 0. * initial or fixed alpha, 0:infinity (constant rate) 43 | Malpha = 0 * different alphas for genes 44 | ncatG = 10 * # of categories in dG of NSsites models 45 | 46 | getSE = 1 * 0: don't want them, 1: want S.E.s of estimates 47 | RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) 48 | 49 | Small_Diff = .45e-6 50 | cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)? 51 | * fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed 52 | method = 0 * Optimization method 0: simultaneous; 1: one branch a time 53 | 54 | * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt., 55 | * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 56 | * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 57 | * 10: blepharisma nu. 58 | * These codes correspond to transl_table 1 to 11 of GENEBANK. 59 | -------------------------------------------------------------------------------- /Preset/CM/M22/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = * sequence data filename 2 | treefile = .TREE * tree structure file name 3 | outfile = M22_mlc * main result file name 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 1 * 0: concise; 1: detailed, 2: too much 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | 13 | * ndata = 10 14 | clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis 15 | aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a 16 | aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) 17 | * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own 18 | 19 | model = 0 20 | * models for codons: 21 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 22 | * models for AAs or codon-translated AAs: 23 | * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F 24 | * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189) 25 | 26 | NSsites = 22 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; 27 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 28 | * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; 29 | * 13:3normal>0 30 | 31 | icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below 32 | Mgene = 0 33 | * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff 34 | * AA: 0:rates, 1:separate 35 | 36 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 37 | kappa = 3 * initial or fixed kappa 38 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 39 | omega = 1 * initial or fixed omega, for codons or codon-based AAs 40 | 41 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 42 | alpha = 0. * initial or fixed alpha, 0:infinity (constant rate) 43 | Malpha = 0 * different alphas for genes 44 | ncatG = 10 * # of categories in dG of NSsites models 45 | 46 | getSE = 1 * 0: don't want them, 1: want S.E.s of estimates 47 | RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) 48 | 49 | Small_Diff = .5e-6 50 | cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)? 51 | * fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed 52 | method = 0 * Optimization method 0: simultaneous; 1: one branch a time 53 | 54 | * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt., 55 | * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 56 | * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 57 | * 10: blepharisma nu. 58 | * These codes correspond to transl_table 1 to 11 of GENEBANK. 59 | -------------------------------------------------------------------------------- /Preset/SM/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/SM/.DS_Store -------------------------------------------------------------------------------- /Preset/SM/M0/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M0.nuc 2 | treefile = M0.trees 3 | outfile = M0_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 0 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M1a/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M1a.nuc 2 | treefile = M1a.trees 3 | outfile = M1a_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 1 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M2a/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M2a.nuc 2 | treefile = M2a.trees 3 | outfile = M2a_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 2 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M3/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M3.nuc 2 | treefile = M3.trees 3 | outfile = M3_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 3 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M7/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M7.nuc 2 | treefile = M7.trees 3 | outfile = M7_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 7 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M8/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M8.nuc 2 | treefile = M8.trees 3 | outfile = M8_mlc 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 0 * 1: detailed output, 0: concise output 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree 13 | aaDist = 0 14 | model = 0 15 | * models for codons: 16 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 17 | 18 | NSsites = 8 * 0:one w;1:neutral;2:selection;3:discrete;4:freqs; 19 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 20 | * 10:beta&gamma+1;11:beta&normal>1;12:0&2normal>1; 21 | * 13:3normal>0 22 | icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below 23 | Mgene = 0 24 | 25 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 26 | kappa = 2 * initial or fixed kappa 27 | fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate 28 | omega = 2 * initial or fixed omega, for codons or codon-transltd AAs 29 | 30 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 31 | alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) 32 | Malpha = 0 * different alphas for genes 33 | ncatG = 3 * # of categories in the dG or AdG models of rates 34 | 35 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 36 | RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) 37 | 38 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 39 | method = 0 * 0: simultaneous; 1: one branch at a time 40 | Small_Diff = .45e-6 41 | cleandata = 1 42 | 43 | * Specifications for duplicating results for the small data set in table 1 44 | * of Yang (1998 MBE 15:568-573). 45 | * see the tree file lysozyme.trees for specification of node (branch) labels 46 | -------------------------------------------------------------------------------- /Preset/SM/M8a/codeml.ctl: -------------------------------------------------------------------------------- 1 | seqfile = M8a.nuc * sequence data filename 2 | treefile = M8a.trees * tree structure file name 3 | outfile = M8a_mlc * main result file name 4 | 5 | noisy = 9 * 0,1,2,3,9: how much rubbish on the screen 6 | verbose = 1 * 0: concise; 1: detailed, 2: too much 7 | runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic 8 | * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise 9 | 10 | seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs 11 | CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table 12 | 13 | * ndata = 10 14 | clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis 15 | aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a 16 | 17 | model = 0 18 | * models for codons: 19 | * 0:one, 1:b, 2:2 or more dN/dS ratios for branches 20 | * models for AAs or codon-translated AAs: 21 | * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F 22 | * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189) 23 | 24 | NSsites = 8 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; 25 | * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ 26 | * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; 27 | * 13:3normal>0 28 | 29 | icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below 30 | Mgene = 0 31 | * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff 32 | * AA: 0:rates, 1:separate 33 | 34 | fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated 35 | kappa = 2 * initial or fixed kappa 36 | fix_omega = 1 * 1: omega or omega_1 fixed, 0: estimate 37 | omega = 1 * initial or fixed omega, for codons or codon-based AAs 38 | 39 | fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha 40 | alpha = 0. * initial or fixed alpha, 0:infinity (constant rate) 41 | Malpha = 0 * different alphas for genes 42 | ncatG = 3 * # of categories in dG of NSsites models 43 | 44 | getSE = 0 * 0: don't want them, 1: want S.E.s of estimates 45 | RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) 46 | 47 | Small_Diff = .45e-6 48 | cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)? 49 | fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed 50 | method = 0 * Optimization method 0: simultaneous; 1: one branch a time 51 | 52 | * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt., 53 | * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 54 | * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 55 | * 10: blepharisma nu. 56 | * These codes correspond to transl_table 1 to 11 of GENEBANK. 57 | -------------------------------------------------------------------------------- /Preset/chi2.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/chi2.exe -------------------------------------------------------------------------------- /Preset/codeml.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Preset/codeml.exe -------------------------------------------------------------------------------- /Quick_Guide.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/Quick_Guide.pdf -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | **1.** **Introduction** 2 | 3 | EasyCodeML is an interactive visual tool for detecting selection in molecular evolutionary analysis. It implements the major codon-based models of CodeML in a simple and user-friendly interface. 4 | 5 | EasyCodeML is written in Java. Precompiled versions are available for Microsoft Windows, Mac OS X, and Linux. We cannot guarantee that EasyCodeML will work well on other operating systems. The lastest version is 1.4. 6 | 7 | **2.** **Citing EasyCodeML** 8 | 9 | The recommended citation for this program is: 10 | 11 | Gao, F., Chen, C., Arab, D.A., Du, Z., He, Y., Ho, S.Y.W., 2019. EasyCodeML: A visual tool for analysis of selection using CodeML. Ecology and Evolution 9, 3891-3898. 12 | 13 | **3.** **System requirements** 14 | 15 | Before running EasyCodeML, please ensure that your computer has a recent version of the Java Runtime Environment (JRE 1.6 or higher). The latest version of Java can be downloaded from http://www.java.com. 16 | 17 | To export a tree as Newick format you will also need a recent version of FigTree (http://tree.bio.ed.ac.uk/software/figtree/). 18 | 19 | **4.** **Data preparation** 20 | 21 | **4.1** **Sequence alignment in PAML format** 22 | 23 | CodeML requires a sequence alignment in PAML format. EasyCodeML includes a utility called Seqformat Convertor, which can automatically convert Clustal, FASTA, MEGA, Nexus, and Phylip formats into PAML format. 24 | 25 | To convert sequence format in batch mode, type the following commands at the command prompt (CMD in windows or Terminal in Mac or Linux). 26 | 27 | Parameter notes： 28 | 29 | The parameters ‘-i’ and ‘-oF’ MUST be supplied and the parameters ‘-o’ and ‘-iF’ are optional. 30 | 31 | java -cp EasyCodeML.jar SeqFormatConvert.seqFactory.SeqConverter -i -oF 32 | 33 | -i the directory to be read in 34 | 35 | -o the output directory 36 | 37 | -iF input sequence format 38 | 39 | -oF output sequence format [fasta (default)|MEGA|nexus|PAMLphylip] 40 | 41 | Example: 42 | 43 | java -cp EasyCodeML.jar SeqFormatConvert.seqFactory.SeqConverter -i /Users/user1/Desktop -oF nexus 44 | 45 | **4.2** **Tree file** **in Newick format** 46 | 47 | The tree file must be in plain Newick format (e.g., Examples/Example1.tree). The tree can not include branch lengths or bootstrap values and each node can have a single label. Taxon names should not have illegal characters (such as spaces and semicolons). 48 | 49 | 50 | 51 | **4.3** **Labelling branches in the phylogenetic tree** 52 | 53 | Tree labelling is necessary when using the branch-related models. To do this, press the ‘Label’ button in EasyCodeML, select the branch or clade to be treated as the foreground lineage, and press “done”. 54 | 55 | ​ In EasyCodeML, the symbols ‘#’ and ‘$’ are used for the branch or branch-site models and for the clade model, respectively. For the branch and clade models, if we have multiple foregroud branches (or clades) to be labelled (no more than 5), press the buttons 1st, 2nd, 3rd, 4th, and 5th to label each foregroud branch (or clade) in turn. 56 | 57 | **5.** **Running the program** 58 | 59 | EasyCodeML provides two different running modes. The first is the preset mode, in which all key parameters of the nested models are built-in and which has pipelines for the selection analyses. The second running mode is the custom mode for experienced users. As with pamlX, the parameters for any codon-based model can be modified to meet different requirements. 60 | 61 | The Quick Guide provides tutorials that illustrate the use of the two running modes. 62 | 63 | 64 | 65 | **6.** **Tools menu in EasyCodeML** 66 | 67 | | **Menu** | **Item** | **Description** | 68 | | -------- | :---------------------- | ------------------------------------------------- | 69 | | File | | | 70 | | | Load Aligned Sequence | Load a codon-based sequence alignment | 71 | | | Load Tree File | Load a tree file in Newick format | 72 | | | Exit | Quit the program | 73 | | Tools | | | 74 | | | LRTs Calculator | Retrieve *p*-values for LRTs | 75 | | | Control File Editor | Edit a CodeML control file | 76 | | | Seqformat Convertor | Convert sequence alignment to PAML format | 77 | | | Tree Cleaner | Convert tree file to NEWICK format | 78 | | Options | | | 79 | | | Configure Tree Label | Modify tree layout to fit in the display window | 80 | | Help | | | 81 | | | About | About EasyCodeML | 82 | | | User guide | Quick Guide for new users | 83 | | | Check for updates | Update to the newest version | 84 | 85 | 86 | 87 | **7.** **Reporting bugs and feedback** 88 | 89 | We welcome bug reports, feedback, and suggestions. For support please contact F. Gao (raindy[at]fafu.edu.cn) or C. Chen (ccj0410[at] gmail.com). 90 | 91 | **8.** **License** 92 | 93 | Copyright 2018 by the EasyCodeML authors. EasyCodeML is freely available to non-commercial users and you are welcome to redistribute it under certain conditions. No guarantee of the functionality of this software, or of the accuracy of results obtained, is expressed or implied. Please inspect any results carefully. 94 | -------------------------------------------------------------------------------- /Version History.txt: -------------------------------------------------------------------------------- 1 | Version 1.41 released 7-May-2023 2 | 3 | What's new in v1.41 4 | 5 | Fixed a bug for the option of 'Run LRTs' 6 | ================================================================================ 7 | Version 1.4 released 25-Apr-2021 8 | 9 | What's new in v1.4 10 | 11 | The option of 'icode' for genetic code selection available in the Preset Mode 12 | ================================================================================ 13 | 14 | Version 1.31 released 22-Oct-2020 15 | 16 | What's new in v1.31 17 | 18 | Add a Tree Cleaner in the Tools Menu to generate Tree file used for CodeML analysis 19 | 20 | ================================================================================ 21 | 22 | EasyCodeML v1.21 23 | 24 | A visual tool for analysis of selection using CodeML 25 | 26 | Presented by F. Gao, C.J. Chen et al. 27 | 28 | Last updated: 25-Aug-2019 29 | 30 | ================================================================================ 31 | 32 | Version 1.21 released 25-Aug-2019 33 | 34 | What's new in v1.21 35 | 36 | (1) Automatically save the profiles to enable all parameters for CodeML analysis 37 | 38 | (2) Add a citaion of EasyCodeML paper published in Ecoclogy and Evolution 39 | ================================================================================ 40 | 41 | Version 1.2 released 01-Feb-2019 42 | 43 | New Features: 44 | 45 | (1) Allows the labelling of multiple foreground branches each time for the branch models; 46 | 47 | (2) Added an update check feature to EasyCodeML (‘Check for updates’ in the ‘Help’ menu); 48 | 49 | (3) Added the M8-M8a comparison in the site models in the preset running mode; 50 | 51 | (4) Added an option allowing users to decide whether or not to run CodeML in slient mode. 52 | -------------------------------------------------------------------------------- /inPath/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/inPath/.DS_Store -------------------------------------------------------------------------------- /inPath/Command line for reference.txt: -------------------------------------------------------------------------------- 1 | Command line for reference: 2 | 3 | java -cp EasyCodeML.jar SeqFormatConvert.seqFactory.SeqConverter -h 4 | 5 | java -cp EasyCodeML.jar SeqFormatConvert.seqFactory.SeqConverter -i inPath -o outPath -oF PAML -------------------------------------------------------------------------------- /inPath/Seq1.fasta: -------------------------------------------------------------------------------- 1 | >Human_ECP 2 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 3 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 4 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGCAATTAACAATTAT 5 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 6 | GTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCGG 7 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 8 | TCAAACTGCACGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 9 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACC 10 | ATC 11 | >Goril_ECP 12 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 13 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 14 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTAT 15 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 16 | GTTTGTGGTAACCAAAGTATACGCTGCCTTCATAACAGAACTCTCAACAATTGTCATCGG 17 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 18 | TCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 19 | AGAGATCCA---CAGGATTCTCCACGGTATCCTGTGGTTCCTGTTCACCTGGATACCACC 20 | ATC 21 | >Chimp_ECP 22 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 23 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 24 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTAT 25 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 26 | GTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCAG 27 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 28 | TCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 29 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATGCCACC 30 | ATC 31 | >Orang_ECP 32 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTAGTGGT 33 | GTGGGGGGCTCACTCCATGCCAAACCCCGACAGTTTACGAGGGCTCAGTGGTTTGCCATC 34 | CAGCACGTCAGTCTGAACCCTCCTCAATGCACCACTGCAATGCGGGTAATTAACAATTAT 35 | CAACGGCGTTGCAAAGACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 36 | GTTTGTGGTAACCCAAATATAACCTGTCCTCGTAACAGAACTCTCCACAATTGTCATCGG 37 | AGTAGATTCCAGGTGCCTTTACTCCACTGTAACCTCACAAATCCAGGTGCACAGAATATT 38 | TCAAACTGCAAGTATGCAGACAGAACAGAAAGGAGGTTCTATGTAGTTGCATGTGACAAC 39 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACC 40 | ATC 41 | >Macaq_ECP 42 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 43 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACAAAGGCTCAGTGGTTTGCCATC 44 | CAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTAT 45 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCATATACAGCTAAT 46 | GTTTGTCGTAACGAACGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGT 47 | AGTAGATACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 48 | TCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGC 49 | AGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCACC 50 | ATC 51 | >Macaq2_ECP 52 | ATGGTTCCAAAACTGTTCACTCCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 53 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAAGGCTCAGTGGTTTGCCATC 54 | CAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTAT 55 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCAAATACAGTTAAT 56 | GTTTGTCGTAACCGAAGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGT 57 | AGTAGCTACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 58 | TCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGC 59 | AGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCATC 60 | ATC 61 | >Orang_EDN 62 | ATGGTTCCAAAACTGTTCACTTCTCAAATTTCCCTGCTTCTTCTGTTGGGGCTTCTGGCT 63 | GTGGACGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 64 | CAGCACATCAATATGACCTCCCAGCAATGCAACAATGCAATGCAGGTCATTAACAATTTT 65 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTGCGTACAACTTTTGCTAATGTAGTTAAT 66 | GTTTGTGGTAACCCAAATATAACCTGTCCTAGTAACAGAAGTCGCAACAATTGTCATCAT 67 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 68 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 69 | AGGGATCCACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 70 | ATC 71 | >Chimp_EDN 72 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCA 73 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 74 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTAT 75 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 76 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAC 77 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 78 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 79 | AGAGATCAACGACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATC 80 | ATC 81 | >Gorilla_EDN 82 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCT 83 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 84 | CAGCACATCAATATGACATCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 85 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 86 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTTGCAAAAATTGTCATCAA 87 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 88 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 89 | AGAGATCAACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 90 | ATC 91 | >Human_EDN 92 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCT 93 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 94 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 95 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 96 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCACCAC 97 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 98 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 99 | AGAGATCAACGACGAGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 100 | ATC 101 | >Hylobates_EDN 102 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 103 | GTGGAGGGCTCACTCCATGCCAAACCCCAACAGTTTACCTGGGCTCAGTGGTTTGAAATC 104 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTAT 105 | CAACGGCGATGCAAAAACCAAAATACTTTTCTTCGTACCACTTTTGCTAATGTAGTTAAT 106 | GTTTGTGGTAACCCAAATATGACATGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAA 107 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 108 | TCAAACTGCGGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 109 | AGAGATCAACGACGGGACCCTCCACAGTATCCAGTAGTTCCGGTTCACCTGGATAGAATC 110 | ATC 111 | >Macaq_EDN 112 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 113 | GTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 114 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 115 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 116 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 117 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 118 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 119 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATC 120 | ATC 121 | >Macaq2_EDN 122 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 123 | GTGGAAGGCTCACTTCATGCCAAACCCAGACAATTTACCTGGGCTCAGTGGTTTGAAATC 124 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 125 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 126 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 127 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 128 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 129 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTC 130 | ATC 131 | >Papio_EDN 132 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 133 | GTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 134 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 135 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 136 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 137 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 138 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 139 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTC 140 | ATC 141 | >Cercopith_EDN 142 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 143 | GTGGAGGGCTCACTCCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 144 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 145 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 146 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 147 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCAAAAT---ATT 148 | TCAAATTGCAAGTATACACAGACAACAGCAAACAAGTTCTACATAGTTGCATGTAACAAC 149 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAGTC 150 | ATC 151 | -------------------------------------------------------------------------------- /inPath/Seq2.meg: -------------------------------------------------------------------------------- 1 | #Mega 2 | !Title None; 3 | 4 | #Human_ECP 5 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 6 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 7 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGCAATTAACAATTAT 8 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 9 | GTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCGG 10 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 11 | TCAAACTGCACGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 12 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACC 13 | ATC 14 | 15 | #Goril_ECP 16 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 17 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 18 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTAT 19 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 20 | GTTTGTGGTAACCAAAGTATACGCTGCCTTCATAACAGAACTCTCAACAATTGTCATCGG 21 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 22 | TCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 23 | AGAGATCCA---CAGGATTCTCCACGGTATCCTGTGGTTCCTGTTCACCTGGATACCACC 24 | ATC 25 | 26 | #Chimp_ECP 27 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 28 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATC 29 | CAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTAT 30 | CGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 31 | GTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCAG 32 | AGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 33 | TCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAAC 34 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATGCCACC 35 | ATC 36 | 37 | #Orang_ECP 38 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTAGTGGT 39 | GTGGGGGGCTCACTCCATGCCAAACCCCGACAGTTTACGAGGGCTCAGTGGTTTGCCATC 40 | CAGCACGTCAGTCTGAACCCTCCTCAATGCACCACTGCAATGCGGGTAATTAACAATTAT 41 | CAACGGCGTTGCAAAGACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAAT 42 | GTTTGTGGTAACCCAAATATAACCTGTCCTCGTAACAGAACTCTCCACAATTGTCATCGG 43 | AGTAGATTCCAGGTGCCTTTACTCCACTGTAACCTCACAAATCCAGGTGCACAGAATATT 44 | TCAAACTGCAAGTATGCAGACAGAACAGAAAGGAGGTTCTATGTAGTTGCATGTGACAAC 45 | AGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACC 46 | ATC 47 | 48 | #Macaq_ECP 49 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 50 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACAAAGGCTCAGTGGTTTGCCATC 51 | CAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTAT 52 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCATATACAGCTAAT 53 | GTTTGTCGTAACGAACGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGT 54 | AGTAGATACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 55 | TCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGC 56 | AGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCACC 57 | ATC 58 | 59 | #Macaq2_ECP 60 | ATGGTTCCAAAACTGTTCACTCCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 61 | GTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAAGGCTCAGTGGTTTGCCATC 62 | CAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTAT 63 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCAAATACAGTTAAT 64 | GTTTGTCGTAACCGAAGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGT 65 | AGTAGCTACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATT 66 | TCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGC 67 | AGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCATC 68 | ATC 69 | 70 | #Orang_EDN 71 | ATGGTTCCAAAACTGTTCACTTCTCAAATTTCCCTGCTTCTTCTGTTGGGGCTTCTGGCT 72 | GTGGACGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 73 | CAGCACATCAATATGACCTCCCAGCAATGCAACAATGCAATGCAGGTCATTAACAATTTT 74 | CAACGGCGTTGCAAAAACCAAAATACTTTTCTGCGTACAACTTTTGCTAATGTAGTTAAT 75 | GTTTGTGGTAACCCAAATATAACCTGTCCTAGTAACAGAAGTCGCAACAATTGTCATCAT 76 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 77 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 78 | AGGGATCCACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 79 | ATC 80 | 81 | #Chimp_EDN 82 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCA 83 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 84 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTAT 85 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 86 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAC 87 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 88 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 89 | AGAGATCAACGACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATC 90 | ATC 91 | 92 | #Gorilla_EDN 93 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCT 94 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 95 | CAGCACATCAATATGACATCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 96 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 97 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTTGCAAAAATTGTCATCAA 98 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 99 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 100 | AGAGATCAACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 101 | ATC 102 | 103 | #Human_EDN 104 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCT 105 | GTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACC 106 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 107 | CAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAAT 108 | GTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCACCAC 109 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 110 | TCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 111 | AGAGATCAACGACGAGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATC 112 | ATC 113 | 114 | #Hylobates_EDN 115 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 116 | GTGGAGGGCTCACTCCATGCCAAACCCCAACAGTTTACCTGGGCTCAGTGGTTTGAAATC 117 | CAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTAT 118 | CAACGGCGATGCAAAAACCAAAATACTTTTCTTCGTACCACTTTTGCTAATGTAGTTAAT 119 | GTTTGTGGTAACCCAAATATGACATGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAA 120 | AGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATT 121 | TCAAACTGCGGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAAC 122 | AGAGATCAACGACGGGACCCTCCACAGTATCCAGTAGTTCCGGTTCACCTGGATAGAATC 123 | ATC 124 | 125 | #Macaq_EDN 126 | ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 127 | GTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 128 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCAGGTCATTAACAATTAT 129 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 130 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 131 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 132 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 133 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATC 134 | ATC 135 | 136 | #Macaq2_EDN 137 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 138 | GTGGAAGGCTCACTTCATGCCAAACCCAGACAATTTACCTGGGCTCAGTGGTTTGAAATC 139 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 140 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 141 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 142 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 143 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 144 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTC 145 | ATC 146 | 147 | #Papio_EDN 148 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 149 | GTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 150 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 151 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 152 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 153 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATT 154 | TCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAAC 155 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTC 156 | ATC 157 | 158 | #Cercopith_EDN 159 | ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGT 160 | GTGGAGGGCTCACTCCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATC 161 | CAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTAT 162 | CAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCAT 163 | GTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCAT 164 | AGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCAAAAT---ATT 165 | TCAAATTGCAAGTATACACAGACAACAGCAAACAAGTTCTACATAGTTGCATGTAACAAC 166 | AGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAGTC 167 | ATC 168 | 169 | -------------------------------------------------------------------------------- /inPath/Seq3.nex: -------------------------------------------------------------------------------- 1 | #NEXUS 2 | 3 | Begin data; 4 | Dimensions ntax=15 nchar=483; 5 | Format datatype=DNA gap=- missing=?; 6 | Matrix 7 | Human_ECP ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGCAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCGGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCACGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACCATC 8 | Goril_ECP ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCTTCATAACAGAACTCTCAACAATTGTCATCGGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CAGGATTCTCCACGGTATCCTGTGGTTCCTGTTCACCTGGATACCACCATC 9 | Chimp_ECP ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACATCAGTCTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATTAACAATTATCGATGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCAAAGTATACGCTGCCCTCATAACAGAACTCTCAACAATTGTCATCAGAGTAGATTCCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAAACTGCAGGTATGCAGACAGACCAGGAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATGCCACCATC 10 | Orang_ECP ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTAGTGGTGTGGGGGGCTCACTCCATGCCAAACCCCGACAGTTTACGAGGGCTCAGTGGTTTGCCATCCAGCACGTCAGTCTGAACCCTCCTCAATGCACCACTGCAATGCGGGTAATTAACAATTATCAACGGCGTTGCAAAGACCAAAATACTTTTCTTCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATAACCTGTCCTCGTAACAGAACTCTCCACAATTGTCATCGGAGTAGATTCCAGGTGCCTTTACTCCACTGTAACCTCACAAATCCAGGTGCACAGAATATTTCAAACTGCAAGTATGCAGACAGAACAGAAAGGAGGTTCTATGTAGTTGCATGTGACAACAGAGATCCA---CGGGATTCTCCACGGTATCCTGTGGTTCCAGTTCACCTGGATACCACCATC 11 | Macaq_ECP ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACAAAGGCTCAGTGGTTTGCCATCCAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTATCAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCATATACAGCTAATGTTTGTCGTAACGAACGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGTAGTAGATACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGCAGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCACCATC 12 | Macaq2_ECP ATGGTTCCAAAACTGTTCACTCCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAGACCCCCACAGTTTACGAAGGCTCAGTGGTTTGCCATCCAGCACATCAATGTGAACCCCCCTCGATGCACCATTGCAATGCGGGTAATAAATAATTATCAACGGCGTTGCAAAAACCAAAATACTTTTCTTCGTACAACTTTTGCAAATACAGTTAATGTTTGTCGTAACCGAAGTATACGCTGCCCTCGTAACAGAACTCTCCACAATTGTCATCGTAGTAGCTACCGGGTGCCTTTACTCCACTGTGACCTCATAAATCCAGGTGCACAGAATATTTCAACCTGCAGGTATGCAGACAGACCAGGACGGAGGTTCTATGTAGTTGCATGTGAAAGCAGAGATCCA---CGGGATTCTCCACGGTATCCAGTGGTTCCAGTTCACCTGGATACCATCATC 13 | Orang_EDN ATGGTTCCAAAACTGTTCACTTCTCAAATTTCCCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGACGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCAACAATGCAATGCAGGTCATTAACAATTTTCAACGGCGTTGCAAAAACCAAAATACTTTTCTGCGTACAACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATAACCTGTCCTAGTAACAGAAGTCGCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGGGATCCACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 14 | Chimp_EDN ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCAGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCATCACAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATCATC 15 | Gorilla_EDN ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACATCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTTGCAAAAATTGTCATCAAAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 16 | Human_EDN ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTCTGGCTGTGGAGGGCTCACTCCATGTCAAACCTCCACAGTTTACCTGGGCTCAATGGTTTGAAACCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTCCTTCTTACAACTTTTGCTAACGTAGTTAATGTTTGTGGTAACCCAAATATGACCTGTCCTAGTAACAAAACTCGCAAAAATTGTCACCACAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCAGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGAGACCCTCCACAGTATCCGGTGGTTCCAGTTCACCTGGATAGAATCATC 17 | Hylobates_EDN ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAAACCCCAACAGTTTACCTGGGCTCAGTGGTTTGAAATCCAGCACATCAATATGACCTCCCAGCAATGCACCAATGCAATGCGGGTCATTAACAATTATCAACGGCGATGCAAAAACCAAAATACTTTTCTTCGTACCACTTTTGCTAATGTAGTTAATGTTTGTGGTAACCCAAATATGACATGTCCTAGTAACAAAACTCGCAAAAATTGTCATCAAAGTGGAAGCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCCACAGAATATTTCAAACTGCGGGTATGCGCAGACACCAGCAAACATGTTCTATATAGTTGCATGTGACAACAGAGATCAACGACGGGACCCTCCACAGTATCCAGTAGTTCCGGTTCACCTGGATAGAATCATC 18 | Macaq_EDN ATGGTTCCAAAACTGTTCACTTCCCAAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCAGGTCATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAATCATC 19 | Macaq2_EDN ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCAGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTCATC 20 | Papio_EDN ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAAGGCTCACTTCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCGAAGG---ATTTCAAATTGCAGGTATACACAGACAACAGCAAACAAGTACTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACTTGGATAGAGTCATC 21 | Cercopith_EDN ATGGTTCCAAAACTGTTCACTTCCCCAATTTGTCTGCTTCTTCTGTTGGGGCTTATGGGTGTGGAGGGCTCACTCCATGCCAAACCCGGACAATTTACCTGGGCTCAGTGGTTTGAAATCCAGCATATAAATATGACCTCTGGCCAATGCACCAATGCAATGCTGGTAATTAACAATTATCAACGGCGATGCAAAAATCAAAATACTTTTCTTCTTACAACTTTTGCTGATGTAGTTCATGTCTGTGGTAACCCAAGCATGCCCTGCCCTAGCAACACAAGTCTCAACAATTGTCATCATAGTGGAGTCCAGGTGCCTTTAATCCACTGTAACCTCACAACTCCAAGTCAAAAT---ATTTCAAATTGCAAGTATACACAGACAACAGCAAACAAGTTCTACATAGTTGCATGTAACAACAGCGATCCAGTACGGGACCCTCCACAGTATCCAGTGGTTCCAGTTCACCTGGATAGAGTCATC 22 | ; 23 | End; 24 | -------------------------------------------------------------------------------- /outPath/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioEasy/EasyCodeML/585b7c9f2ac4cc0eb13b01aa0279bb8f18c3da57/outPath/.DS_Store -------------------------------------------------------------------------------- /outPath/Seq1.pml: -------------------------------------------------------------------------------- 1 | 15 483 2 | Human_ECP 3 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGCAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCACGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 4 | Goril_ECP 5 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCUUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CAGGAUUCUCCACGGUAUCCUGUGGUUCCUGUUCACCUGGAUACCACCAUC 6 | Chimp_ECP 7 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCAGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUGCCACCAUC 8 | Orang_ECP 9 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAGUGGUGUGGGGGGCUCACUCCAUGCCAAACCCCGACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACGUCAGUCUGAACCCUCCUCAAUGCACCACUGCAAUGCGGGUAAUUAACAAUUAUCAACGGCGUUGCAAAGACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUCGUAACAGAACUCUCCACAAUUGUCAUCGGAGUAGAUUCCAGGUGCCUUUACUCCACUGUAACCUCACAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAAGUAUGCAGACAGAACAGAAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 10 | Macaq_ECP 11 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACAAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAUAUACAGCUAAUGUUUGUCGUAACGAACGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGAUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCACCAUC 12 | Macaq2_ECP 13 | AUGGUUCCAAAACUGUUCACUCCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAAAUACAGUUAAUGUUUGUCGUAACCGAAGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGCUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCAUCAUC 14 | Orang_EDN 15 | AUGGUUCCAAAACUGUUCACUUCUCAAAUUUCCCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGACGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCAACAAUGCAAUGCAGGUCAUUAACAAUUUUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUGCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUAGUAACAGAAGUCGCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGGGAUCCACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 16 | Chimp_EDN 17 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCAGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 18 | Gorilla_EDN 19 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACAUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUUGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 20 | Human_EDN 21 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCACCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGAGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 22 | Hylobates_EDN 23 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCCAACAGUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUUCUUCGUACCACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACAUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCGGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUAGUUCCGGUUCACCUGGAUAGAAUCAUC 24 | Macaq_EDN 25 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 26 | Macaq2_EDN 27 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCAGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 28 | Papio_EDN 29 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 30 | Cercopith_EDN 31 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCAAAAU---AUUUCAAAUUGCAAGUAUACACAGACAACAGCAAACAAGUUCUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAGUCAUC 32 | -------------------------------------------------------------------------------- /outPath/Seq2.pml: -------------------------------------------------------------------------------- 1 | 15 483 2 | Human_ECP 3 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGCAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCACGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 4 | Goril_ECP 5 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCUUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CAGGAUUCUCCACGGUAUCCUGUGGUUCCUGUUCACCUGGAUACCACCAUC 6 | Chimp_ECP 7 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCAGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUGCCACCAUC 8 | Orang_ECP 9 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAGUGGUGUGGGGGGCUCACUCCAUGCCAAACCCCGACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACGUCAGUCUGAACCCUCCUCAAUGCACCACUGCAAUGCGGGUAAUUAACAAUUAUCAACGGCGUUGCAAAGACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUCGUAACAGAACUCUCCACAAUUGUCAUCGGAGUAGAUUCCAGGUGCCUUUACUCCACUGUAACCUCACAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAAGUAUGCAGACAGAACAGAAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 10 | Macaq_ECP 11 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACAAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAUAUACAGCUAAUGUUUGUCGUAACGAACGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGAUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCACCAUC 12 | Macaq2_ECP 13 | AUGGUUCCAAAACUGUUCACUCCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAAAUACAGUUAAUGUUUGUCGUAACCGAAGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGCUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCAUCAUC 14 | Orang_EDN 15 | AUGGUUCCAAAACUGUUCACUUCUCAAAUUUCCCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGACGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCAACAAUGCAAUGCAGGUCAUUAACAAUUUUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUGCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUAGUAACAGAAGUCGCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGGGAUCCACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 16 | Chimp_EDN 17 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCAGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 18 | Gorilla_EDN 19 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACAUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUUGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 20 | Human_EDN 21 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCACCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGAGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 22 | Hylobates_EDN 23 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCCAACAGUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUUCUUCGUACCACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACAUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCGGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUAGUUCCGGUUCACCUGGAUAGAAUCAUC 24 | Macaq_EDN 25 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 26 | Macaq2_EDN 27 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCAGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 28 | Papio_EDN 29 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 30 | Cercopith_EDN 31 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCAAAAU---AUUUCAAAUUGCAAGUAUACACAGACAACAGCAAACAAGUUCUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAGUCAUC 32 | -------------------------------------------------------------------------------- /outPath/Seq3.pml: -------------------------------------------------------------------------------- 1 | 15 483 2 | Human_ECP 3 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGCAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCACGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 4 | Goril_ECP 5 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCUUCAUAACAGAACUCUCAACAAUUGUCAUCGGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CAGGAUUCUCCACGGUAUCCUGUGGUUCCUGUUCACCUGGAUACCACCAUC 6 | Chimp_ECP 7 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACAUCAGUCUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUUAACAAUUAUCGAUGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCAAAGUAUACGCUGCCCUCAUAACAGAACUCUCAACAAUUGUCAUCAGAGUAGAUUCCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAGGUAUGCAGACAGACCAGGAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUGCCACCAUC 8 | Orang_ECP 9 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAGUGGUGUGGGGGGCUCACUCCAUGCCAAACCCCGACAGUUUACGAGGGCUCAGUGGUUUGCCAUCCAGCACGUCAGUCUGAACCCUCCUCAAUGCACCACUGCAAUGCGGGUAAUUAACAAUUAUCAACGGCGUUGCAAAGACCAAAAUACUUUUCUUCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUCGUAACAGAACUCUCCACAAUUGUCAUCGGAGUAGAUUCCAGGUGCCUUUACUCCACUGUAACCUCACAAAUCCAGGUGCACAGAAUAUUUCAAACUGCAAGUAUGCAGACAGAACAGAAAGGAGGUUCUAUGUAGUUGCAUGUGACAACAGAGAUCCA---CGGGAUUCUCCACGGUAUCCUGUGGUUCCAGUUCACCUGGAUACCACCAUC 10 | Macaq_ECP 11 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACAAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAUAUACAGCUAAUGUUUGUCGUAACGAACGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGAUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCACCAUC 12 | Macaq2_ECP 13 | AUGGUUCCAAAACUGUUCACUCCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAGACCCCCACAGUUUACGAAGGCUCAGUGGUUUGCCAUCCAGCACAUCAAUGUGAACCCCCCUCGAUGCACCAUUGCAAUGCGGGUAAUAAAUAAUUAUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUUCGUACAACUUUUGCAAAUACAGUUAAUGUUUGUCGUAACCGAAGUAUACGCUGCCCUCGUAACAGAACUCUCCACAAUUGUCAUCGUAGUAGCUACCGGGUGCCUUUACUCCACUGUGACCUCAUAAAUCCAGGUGCACAGAAUAUUUCAACCUGCAGGUAUGCAGACAGACCAGGACGGAGGUUCUAUGUAGUUGCAUGUGAAAGCAGAGAUCCA---CGGGAUUCUCCACGGUAUCCAGUGGUUCCAGUUCACCUGGAUACCAUCAUC 14 | Orang_EDN 15 | AUGGUUCCAAAACUGUUCACUUCUCAAAUUUCCCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGACGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCAACAAUGCAAUGCAGGUCAUUAACAAUUUUCAACGGCGUUGCAAAAACCAAAAUACUUUUCUGCGUACAACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUAACCUGUCCUAGUAACAGAAGUCGCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGGGAUCCACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 16 | Chimp_EDN 17 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCAGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 18 | Gorilla_EDN 19 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACAUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUUGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 20 | Human_EDN 21 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUCUGGCUGUGGAGGGCUCACUCCAUGUCAAACCUCCACAGUUUACCUGGGCUCAAUGGUUUGAAACCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUCCUUCUUACAACUUUUGCUAACGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACCUGUCCUAGUAACAAAACUCGCAAAAAUUGUCACCACAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCAGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGAGACCCUCCACAGUAUCCGGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 22 | Hylobates_EDN 23 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCCAACAGUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCACAUCAAUAUGACCUCCCAGCAAUGCACCAAUGCAAUGCGGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAACCAAAAUACUUUUCUUCGUACCACUUUUGCUAAUGUAGUUAAUGUUUGUGGUAACCCAAAUAUGACAUGUCCUAGUAACAAAACUCGCAAAAAUUGUCAUCAAAGUGGAAGCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCCACAGAAUAUUUCAAACUGCGGGUAUGCGCAGACACCAGCAAACAUGUUCUAUAUAGUUGCAUGUGACAACAGAGAUCAACGACGGGACCCUCCACAGUAUCCAGUAGUUCCGGUUCACCUGGAUAGAAUCAUC 24 | Macaq_EDN 25 | AUGGUUCCAAAACUGUUCACUUCCCAAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCAGGUCAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAAUCAUC 26 | Macaq2_EDN 27 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCAGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 28 | Papio_EDN 29 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAAGGCUCACUUCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCGAAGG---AUUUCAAAUUGCAGGUAUACACAGACAACAGCAAACAAGUACUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACUUGGAUAGAGUCAUC 30 | Cercopith_EDN 31 | AUGGUUCCAAAACUGUUCACUUCCCCAAUUUGUCUGCUUCUUCUGUUGGGGCUUAUGGGUGUGGAGGGCUCACUCCAUGCCAAACCCGGACAAUUUACCUGGGCUCAGUGGUUUGAAAUCCAGCAUAUAAAUAUGACCUCUGGCCAAUGCACCAAUGCAAUGCUGGUAAUUAACAAUUAUCAACGGCGAUGCAAAAAUCAAAAUACUUUUCUUCUUACAACUUUUGCUGAUGUAGUUCAUGUCUGUGGUAACCCAAGCAUGCCCUGCCCUAGCAACACAAGUCUCAACAAUUGUCAUCAUAGUGGAGUCCAGGUGCCUUUAAUCCACUGUAACCUCACAACUCCAAGUCAAAAU---AUUUCAAAUUGCAAGUAUACACAGACAACAGCAAACAAGUUCUACAUAGUUGCAUGUAACAACAGCGAUCCAGUACGGGACCCUCCACAGUAUCCAGUGGUUCCAGUUCACCUGGAUAGAGUCAUC 32 | --------------------------------------------------------------------------------