/AminoAcidMatrices.R
R | 942 lines | 165 code | 49 blank | 728 comment | 0 complexity | 13d32c17283616ebfc6ed0ae0ff30201 MD5 | raw file
1## 2## Copyright 2009 Botond Sipos 3## See the package description for licensing information. 4 5## 6## cpREV 7## 8##########################################################################/** 9# 10# @RdocClass cpREV 11# 12# @title "The cpREV empirical amino acid substitution model" 13# 14# \description{ 15# 16# 17# @classhierarchy 18# } 19# 20# \references{ 21# Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa (2000) Plastid 22# genome phylogeny and a model of amino acid substitution for proteins 23# encoded by chloroplast DNA - Journal of Molecular Evolution 50:348--358 24# DOI: 10.1007/s002399910038 \url{http://bit.ly/bnBVLm} 25# } 26# 27# @synopsis 28# 29# \arguments{ 30# \item{equ.dist}{Equilibrium distribution.} 31# \item{...}{Not used.} 32# } 33# 34# \section{Fields and Methods}{ 35# @allmethods 36# } 37# 38# \examples{ 39# # create substitution model object 40# p<-cpREV() 41# # get object summary 42# summary(p) 43# # display a bubble plot 44# plot(p) 45# 46# # The following code demonstrates how to use 47# # the process in a simulation. 48# 49# # create a sequence, attach process p 50# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 51# # sample states 52# sampleStates(s) 53# # make the first three positions invariable 54# setRateMultipliers(s,p,0,1:3) 55# # get rate multipliers 56# getRateMultipliers(s,p) 57# # create a simulation object 58# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 59# # run simulation 60# Simulate(sim) 61# # print alignment 62# sim$alignment 63# } 64# 65# @author 66# 67# \seealso{ 68# AminoAcidSubst GeneralSubstitution UNREST 69# } 70# 71#*/########################################################################### 72setConstructorS3( 73 "cpREV", 74 function( 75 equ.dist=NA, 76 ... 77 ){ 78 79 this<-AminoAcidSubst$newAAMatrix( 80 name="cpREV", 81 paml.file="cpREV.dat", 82 equ.dist=equ.dist 83 ); 84 85 return(this); 86 87 }, 88 enforceRCC=FALSE 89); 90 91## 92## PAM 93## 94##########################################################################/** 95# 96# @RdocClass PAM 97# 98# @title "The PAM empirical amino acid substitution model" 99# 100# \description{ 101# 102# 103# @classhierarchy 104# } 105# 106# \references{ 107# Dayhoff, M. O.; Schwartz, R. M.; Orcutt, B. C. (1978). "A model of evolutionary change in proteins" - 108# Atlas of Protein Sequence and Structure 5 (3):345-352 109# 110# } 111# 112# @synopsis 113# 114# \arguments{ 115# \item{equ.dist}{Equilibrium distribution.} 116# \item{...}{Not used.} 117# } 118# 119# \section{Fields and Methods}{ 120# @allmethods 121# } 122# 123# \examples{ 124# # create substitution model object 125# p<-PAM() 126# # get object summary 127# summary(p) 128# # display a bubble plot 129# plot(p) 130# 131# # The following code demonstrates how to use 132# # the process in a simulation. 133# 134# # create a sequence, attach process p 135# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 136# # sample states 137# sampleStates(s) 138# # make the first three positions invariable 139# setRateMultipliers(s,p,0,1:3) 140# # get rate multipliers 141# getRateMultipliers(s,p) 142# # create a simulation object 143# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 144# # run simulation 145# Simulate(sim) 146# # print alignment 147# sim$alignment 148# } 149# 150# @author 151# 152# \seealso{ 153# AminoAcidSubst GeneralSubstitution UNREST 154# } 155# 156#*/########################################################################### 157setConstructorS3( 158 "PAM", 159 function( 160 equ.dist=NA, 161 ... 162 ){ 163 164 this<-AminoAcidSubst$newAAMatrix( 165 name="PAM", 166 paml.file="dayhoff.dat", 167 equ.dist=equ.dist 168 ); 169 170 return(this); 171 172 }, 173 enforceRCC=FALSE 174); 175 176## 177## PAM-dcmut 178## 179##########################################################################/** 180# 181# @RdocClass PAM.dcmut 182# 183# @title "The PAM.dcmut empirical amino acid substitution model" 184# 185# \description{ 186# 187# 188# @classhierarchy 189# } 190# 191# \references{ 192# Kosiol, C, and Goldman, N (2005) Different versions of the Dayhoff rate matrix - 193# Molecular Biology and Evolution 22:193-199 \url{http://dx.doi.org/10.1093/molbev/msi005} 194# } 195# 196# @synopsis 197# 198# \arguments{ 199# \item{equ.dist}{Equilibrium distribution.} 200# \item{...}{Not used.} 201# } 202# 203# \section{Fields and Methods}{ 204# @allmethods 205# } 206# 207# \examples{ 208# # create substitution model object 209# p<-PAM.dcmut() 210# # get object summary 211# summary(p) 212# # display a bubble plot 213# plot(p) 214# 215# # The following code demonstrates how to use 216# # the process in a simulation. 217# 218# # create a sequence, attach process p 219# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 220# # sample states 221# sampleStates(s) 222# # make the first three invariable 223# setRateMultipliers(s,p,0,1:3) 224# # get rate multipliers 225# getRateMultipliers(s,p) 226# # create a simulation object 227# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 228# # run simulation 229# Simulate(sim) 230# # print alignment 231# sim$alignment 232# } 233# 234# @author 235# 236# \seealso{ 237# AminoAcidSubst GeneralSubstitution UNREST 238# } 239# 240#*/########################################################################### 241setConstructorS3( 242 "PAM.dcmut", 243 function( 244 equ.dist=NA, 245 ... 246 ){ 247 248 this<-AminoAcidSubst$newAAMatrix( 249 name="PAM.dcmut", 250 paml.file="dayhoff-dcmut.dat", 251 equ.dist=equ.dist 252 ); 253 254 return(this); 255 256 }, 257 enforceRCC=FALSE 258); 259 260## 261## JTT 262## 263##########################################################################/** 264# 265# @RdocClass JTT 266# 267# @title "The JTT empirical amino acid substitution model" 268# 269# \description{ 270# 271# 272# @classhierarchy 273# } 274# 275# \references{ 276# Jones, D. T., W. R. Taylor, and J. M. Thornton (1992) The rapid generation of mutation data matrices 277# from protein sequences. CABIOS 8:275-282 \url{http://dx.doi.org/10.1093/bioinformatics/8.3.275} 278# } 279# 280# @synopsis 281# 282# \arguments{ 283# \item{equ.dist}{Equilibrium distribution.} 284# \item{...}{Not used.} 285# } 286# 287# \section{Fields and Methods}{ 288# @allmethods 289# } 290# 291# \examples{ 292# # create substitution model object 293# p<-JTT() 294# # get object summary 295# summary(p) 296# # display a bubble plot 297# plot(p) 298# 299# # The following code demonstrates how to use 300# # the process in a simulation. 301# 302# # create a sequence, attach process p 303# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 304# # sample states 305# sampleStates(s) 306# # make the first three positions invariable 307# setRateMultipliers(s,p,0,1:3) 308# # get rate multipliers 309# getRateMultipliers(s,p) 310# # create a simulation object 311# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 312# # run simulation 313# Simulate(sim) 314# # print alignment 315# sim$alignment 316# } 317# 318# @author 319# 320# \seealso{ 321# AminoAcidSubst GeneralSubstitution UNREST 322# } 323# 324#*/########################################################################### 325setConstructorS3( 326 "JTT", 327 function( 328 equ.dist=NA, 329 ... 330 ){ 331 332 this<-AminoAcidSubst$newAAMatrix( 333 name="JTT", 334 paml.file="jones.dat", 335 equ.dist=equ.dist 336 ); 337 338 return(this); 339 340 }, 341 enforceRCC=FALSE 342); 343 344## 345## JTT.dcmut 346## 347##########################################################################/** 348# 349# @RdocClass JTT.dcmut 350# 351# @title "The JTT.dcmut empirical amino acid substitution model" 352# 353# \description{ 354# 355# 356# @classhierarchy 357# } 358# 359# \references{ 360# Kosiol, C, and Goldman, N (2005) Different versions of the Dayhoff rate matrix - 361# Molecular Biology and Evolution 22:193-199 \url{http://dx.doi.org/10.1093/molbev/msi005} 362# 363# Jones, D. T., W. R. Taylor, and J. M. Thornton (1992) The rapid generation of mutation data matrices 364# from protein sequences. CABIOS 8:275-282 \url{http://dx.doi.org/10.1093/bioinformatics/8.3.275} 365# } 366# 367# @synopsis 368# 369# \arguments{ 370# \item{equ.dist}{Equilibrium distribution.} 371# \item{...}{Not used.} 372# } 373# 374# \section{Fields and Methods}{ 375# @allmethods 376# } 377# 378# \examples{ 379# # create substitution model object 380# p<-JTT.dcmut() 381# # get object summary 382# summary(p) 383# # display a bubble plot 384# plot(p) 385# 386# # The following code demonstrates how to use 387# # the process in a simulation. 388# 389# # create a sequence, attach process p 390# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 391# # sample states 392# sampleStates(s) 393# # make the first threee positions invariable 394# setRateMultipliers(s,p,0,1:3) 395# # get rate multipliers 396# getRateMultipliers(s,p) 397# # create a simulation object 398# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 399# # run simulation 400# Simulate(sim) 401# # print alignment 402# sim$alignment 403# } 404# 405# @author 406# 407# \seealso{ 408# AminoAcidSubst GeneralSubstitution UNREST 409# } 410# 411#*/########################################################################### 412setConstructorS3( 413 "JTT.dcmut", 414 function( 415 equ.dist=NA, 416 ... 417 ){ 418 419 this<-AminoAcidSubst$newAAMatrix( 420 name="JTT.dcmut", 421 paml.file="jones-dcmut.dat", 422 equ.dist=equ.dist 423 ); 424 425 return(this); 426 427 }, 428 enforceRCC=FALSE 429); 430 431## 432## LG 433## 434##########################################################################/** 435# 436# @RdocClass LG 437# 438# @title "The LG empirical amino acid substitution model" 439# 440# \description{ 441# 442# 443# @classhierarchy 444# } 445# 446# \references{ 447# Le, S. Q., and O. Gascuel (2008) An improved general amino acid replacement matrix - 448# Mol. Biol. Evol. 25:1307-1320 \url{http://dx.doi.org/10.1093/molbev/msn067} 449# } 450# 451# @synopsis 452# 453# \arguments{ 454# \item{equ.dist}{Equilibrium distribution.} 455# \item{...}{Not used.} 456# } 457# 458# \section{Fields and Methods}{ 459# @allmethods 460# } 461# 462# \examples{ 463# # create substitution model object 464# p<-LG() 465# # get object summary 466# summary(p) 467# # display a bubble plot 468# plot(p) 469# 470# # The following code demonstrates how to use 471# # the process in a simulation. 472# 473# # create a sequence, attach process p 474# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 475# # sample states 476# sampleStates(s) 477# # make the first three positions invariable 478# setRateMultipliers(s,p,0,1:3) 479# # get rate multipliers 480# getRateMultipliers(s,p) 481# # create a simulation object 482# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 483# # run simulation 484# Simulate(sim) 485# # print alignment 486# sim$alignment 487# } 488# 489# @author 490# 491# \seealso{ 492# AminoAcidSubst GeneralSubstitution UNREST 493# } 494# 495#*/########################################################################### 496setConstructorS3( 497 "LG", 498 function( 499 equ.dist=NA, 500 ... 501 ){ 502 503 this<-AminoAcidSubst$newAAMatrix( 504 name="LG", 505 paml.file="lg.dat", 506 equ.dist=equ.dist 507 ); 508 509 return(this); 510 511 }, 512 enforceRCC=FALSE 513); 514 515## 516## mtArt 517## 518##########################################################################/** 519# 520# @RdocClass mtArt 521# 522# @title "The mtArt empirical amino acid substitution model" 523# 524# \description{ 525# 526# 527# @classhierarchy 528# } 529# 530# \references{ 531# Abascal, F., D. Posada, and R. Zardoya (2007) MtArt: A new Model of 532# amino acid replacement for Arthropoda - Mol. Biol. Evol. 24:1-5 \url{http://dx.doi.org/10.1093/molbev/msl136} 533# 534# } 535# 536# @synopsis 537# 538# \arguments{ 539# \item{equ.dist}{Equilibrium distribution.} 540# \item{...}{Not used.} 541# } 542# 543# \section{Fields and Methods}{ 544# @allmethods 545# } 546# 547# \examples{ 548# # create substitution model object 549# p<-mtArt() 550# # get object summary 551# summary(p) 552# # display a bubble plot 553# plot(p) 554# 555# # The following code demonstrates how to use 556# # the process in a simulation. 557# 558# # create a sequence, attach process p 559# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 560# # sample states 561# sampleStates(s) 562# # make the first three positions invariable 563# setRateMultipliers(s,p,0,1:3) 564# # get rate multipliers 565# getRateMultipliers(s,p) 566# # create a simulation object 567# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 568# # run simulation 569# Simulate(sim) 570# # print alignment 571# sim$alignment 572# } 573# 574# @author 575# 576# \seealso{ 577# AminoAcidSubst GeneralSubstitution UNREST 578# } 579# 580#*/########################################################################### 581setConstructorS3( 582 "mtArt", 583 function( 584 equ.dist=NA, 585 ... 586 ){ 587 588 this<-AminoAcidSubst$newAAMatrix( 589 name="mtArt", 590 paml.file="mtArt.dat", 591 equ.dist=equ.dist 592 ); 593 594 return(this); 595 596 }, 597 enforceRCC=FALSE 598); 599 600## 601## mtMam 602## 603##########################################################################/** 604# 605# @RdocClass mtMam 606# 607# @title "The mtMam empirical amino acid substitution model" 608# 609# \description{ 610# 611# 612# @classhierarchy 613# } 614# 615# \references{ 616# Yang, Z., R. Nielsen, and M. Hasegawa (1998) Models of amino acid 617# substitution and applications to Mitochondrial protein evolution, 618# Molecular Biology and Evolution 15:1600-1611 \url{http://bit.ly/by4NMb} 619# } 620# 621# @synopsis 622# 623# \arguments{ 624# \item{equ.dist}{Equilibrium distribution.} 625# \item{...}{Not used.} 626# } 627# 628# \section{Fields and Methods}{ 629# @allmethods 630# } 631# 632# \examples{ 633# # create substitution model object 634# p<-mtMam() 635# # get object summary 636# summary(p) 637# # display a bubble plot 638# plot(p) 639# 640# # The following code demonstrates how to use 641# # the process in a simulation. 642# 643# # create a sequence, attach process p 644# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 645# # sample states 646# sampleStates(s) 647# # make the first three positions invariable 648# setRateMultipliers(s,p,0,1:3) 649# # get rate multipliers 650# getRateMultipliers(s,p) 651# # create a simulation object 652# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 653# # run simulation 654# Simulate(sim) 655# # print alignment 656# sim$alignment 657# } 658# 659# @author 660# 661# \seealso{ 662# AminoAcidSubst GeneralSubstitution UNREST 663# } 664# 665#*/########################################################################### 666setConstructorS3( 667 "mtMam", 668 function( 669 equ.dist=NA, 670 ... 671 ){ 672 673 this<-AminoAcidSubst$newAAMatrix( 674 name="mtMam", 675 paml.file="mtmam.dat", 676 equ.dist=equ.dist 677 ); 678 679 return(this); 680 681 }, 682 enforceRCC=FALSE 683); 684 685## 686## mtREV24 687## 688##########################################################################/** 689# 690# @RdocClass mtREV24 691# 692# @title "The mtREV24 empirical amino acid substitution model" 693# 694# \description{ 695# 696# 697# @classhierarchy 698# } 699# 700# \references{ 701# Adachi, J. and Hasegawa, M. (1996) MOLPHY version 2.3: programs for 702# molecular phylogenetics based on maximum likelihood. Computer Science 703# Monographs of Institute of Statistical Mathematics 28:1-150 704# } 705# 706# @synopsis 707# 708# \arguments{ 709# \item{equ.dist}{Equilibrium distribution.} 710# \item{...}{Not used.} 711# } 712# 713# \section{Fields and Methods}{ 714# @allmethods 715# } 716# 717# \examples{ 718# # create substitution model object 719# p<-mtREV24() 720# # get object summary 721# summary(p) 722# # display a bubble plot 723# plot(p) 724# 725# # The following code demonstrates how to use 726# # the process in a simulation. 727# 728# # create a sequence, attach process p 729# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 730# # sample states 731# sampleStates(s) 732# # make the first three positions invariable 733# setRateMultipliers(s,p,0,1:3) 734# # get rate multipliers 735# getRateMultipliers(s,p) 736# # create a simulation object 737# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 738# # run simulation 739# Simulate(sim) 740# # print alignment 741# sim$alignment 742# } 743# 744# @author 745# 746# \seealso{ 747# AminoAcidSubst GeneralSubstitution UNREST 748# } 749# 750#*/########################################################################### 751setConstructorS3( 752 "mtREV24", 753 function( 754 equ.dist=NA, 755 ... 756 ){ 757 758 this<-AminoAcidSubst$newAAMatrix( 759 name="mtREV24", 760 paml.file="mtREV24.dat", 761 equ.dist=equ.dist 762 ); 763 764 return(this); 765 766 }, 767 enforceRCC=FALSE 768); 769 770## 771## MtZoa 772## 773##########################################################################/** 774# 775# @RdocClass MtZoa 776# 777# @title "The MtZoa empirical amino acid substitution model" 778# 779# \description{ 780# 781# 782# @classhierarchy 783# } 784# 785# \references{ 786# Rota-Stabelli, O., Z. Yang, and M. Telford. (2009) MtZoa: a general mitochondrial amino acid 787# substitutions model for animal evolutionary studies. Mol. Phyl. Evol 52(1):268-72 \url{http://bit.ly/bjZfKi} 788# } 789# 790# @synopsis 791# 792# \arguments{ 793# \item{equ.dist}{Equilibrium distribution.} 794# \item{...}{Not used.} 795# } 796# 797# \section{Fields and Methods}{ 798# @allmethods 799# } 800# 801# \examples{ 802# # create substitution model object 803# p<-MtZoa() 804# # get object summary 805# summary(p) 806# # display a bubble plot 807# plot(p) 808# 809# # The following code demonstrates how to use 810# # the process in a simulation. 811# 812# # create a sequence, attach process p 813# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 814# # sample states 815# sampleStates(s) 816# # make the first three positions invariable 817# setRateMultipliers(s,p,0,1:3) 818# # get rate multipliers 819# getRateMultipliers(s,p) 820# # create a simulation object 821# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 822# # run simulation 823# Simulate(sim) 824# # print alignment 825# sim$alignment 826# } 827# 828# @author 829# 830# \seealso{ 831# AminoAcidSubst GeneralSubstitution UNREST 832# } 833# 834#*/########################################################################### 835setConstructorS3( 836 "MtZoa", 837 function( 838 equ.dist=NA, 839 ... 840 ){ 841 842 this<-AminoAcidSubst$newAAMatrix( 843 name="MtZoa", 844 paml.file="MtZoa.dat", 845 equ.dist=equ.dist 846 ); 847 848 return(this); 849 850 }, 851 enforceRCC=FALSE 852); 853 854## 855## WAG 856## 857##########################################################################/** 858# 859# @RdocClass WAG 860# 861# @title "The WAG empirical amino acid substitution model" 862# 863# \description{ 864# 865# 866# @classhierarchy 867# } 868# 869# \references{ 870# Whelan, S. and N. Goldman (2001) A general empirical model of 871# protein evolution derived from multiple protein families using a maximum likelihood 872# approach - Molecular Biology and Evolution 18:691-699 \url{http://bit.ly/dpTKAd} 873# } 874# 875# @synopsis 876# 877# \arguments{ 878# \item{equ.dist}{Equilibrium distribution.} 879# \item{...}{Not used.} 880# } 881# 882# \section{Fields and Methods}{ 883# @allmethods 884# } 885# 886# \examples{ 887# # create substitution model object 888# p<-WAG() 889# # get object summary 890# summary(p) 891# # display a bubble plot 892# plot(p) 893# 894# # The following code demonstrates how to use 895# # the process in a simulation. 896# 897# # create a sequence, attach process p 898# s<-AminoAcidSequence(length=10,processes=list(list(p)) ) 899# # sample states 900# sampleStates(s) 901# # make the first three positions invariable 902# setRateMultipliers(s,p,0,1:3) 903# # get rate multipliers 904# getRateMultipliers(s,p) 905# # create a simulation object 906# sim<-PhyloSim(root.seq=s,phylo=rcoal(2)) 907# # run simulation 908# Simulate(sim) 909# # print alignment 910# sim$alignment 911# } 912# 913# @author 914# 915# \seealso{ 916# AminoAcidSubst GeneralSubstitution UNREST 917# } 918# 919#*/########################################################################### 920setConstructorS3( 921 "WAG", 922 function( 923 equ.dist=NA, 924 ... 925 ){ 926 927 this<-AminoAcidSubst$newAAMatrix( 928 name="WAG", 929 paml.file="wag.dat", 930 equ.dist=equ.dist 931 ); 932 return(this); 933 934 }, 935 enforceRCC=FALSE 936); 937 938 939 940 941 942