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Table 5 Reduced-state alphabet definitions.

From: Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(A) Rationally defined alphabets
Alphabet Identifier States   
CHARGE_2 KRDE;ACFGHILMNPQSTVWY   
CHARGE_HIS_2 KRDEH;ACFGILMNPPQSTVWY   
CHARGE_3 KR;DE;ACFGHILMNPQSTVWY   
CHARGE_HIS_3 KRH;DE;ACFGILMNPQSTVWY   
SIZE_2 GAVLISPTCND;MFYWQKHRE   
POLARITY_HIS_4 DE;RHK;AILMFPWV;GSTCYNQ   
HYDROPATHY_3 RKDENQH;YWSTG;PAMCFLVI   
(B) Heuristically defined 'Atchley-factor' alphabets
Alphabet Identifier States Alphabet Identifier States
A1_2 CVILFMWAGS;TPYHQNDERK A1_3 CVILFMW;AGSTPY;HQNDERK
A1_4 CVILF;MWAGS;TPYHQ;NDERK A1_5 CVIL;FMWA;GSTP;YHQN;DERK
A1_6 CVI;LFMW;AGS;TPY;HQND;ERK A1_7 CVI;LFM;WAG;ST;PYH;QND;ERK
A1_8 CVI;LF;MWA;GS;TPY;HQ;NDE;RK A1_9 CV;IL;FMW;AG;ST;PY;HQN;DE;RK
A1_10 CV;IL;FM;WA;GS;TP;YH;QN;DE;RK   
A2_2 MEALFKIHVQ;RWDTCNYSGP A2_3 MEALFKI;HVQRWD;TCNYSGP
A2_4 MEALF;KIHVQ;RWDTC;NYSGP A2_5 MEAL;FKIH;VQRW;DTCN;YSGP
A2_6 MEA;LFKI;HVQ;RWD;TCNY;SGP A2_7 MEA;LFK;IHV;QR;WDT;CNY;SGP
A2_8 MEA;LF;KIH;VQ;RWD;TC;NYS;GP A2_9 ME;AL;FKI;HV;QR;WD;TCN;YS;GP
A2_10 ME;AL;FK;IH;VQ;RW;DT;CN;YS;GP   
A3_2 SDQHPLCAVK;WNGERFITMY A3_3 SDQHPLC;AVKWNG;ERFITMY
A3_4 SDQHP;LCAVK;WNGER;FITMY A3_5 SDQH;PLCA;VKWN;GERF;ITMY
A3_6 SDQ;HPLC;AVK;WNG;ERFI;TMY A3_7 SDQ;HPL;CAV;KW;NGE;RFI;TMY
A3_8 SDQ;HP;LCA;VK;WNG;ER;FIT;MY A3_9 SD;QH;PLC;AV;KW;NG;ERF;IT;MY
A3_10 SD;QH;PL;CA;VK;WN;GE;RF;IT;MY   
A4_2 WHCMYQFKDN;EIPRSTGVLA A4_3 WHCMYQF;KDNEIP;RSTGVLA
A4_4 WHCMY;QFKDN;EIPRS;TGVLA A4_5 WHCM;YQFK;DNEI;PRST;GVLA
A4_6 WHC;MYQF;KDN;EIP;RSTG;VLA A4_7 WHC;MYQ;FKD;NE;IPR;STG;VLA
A4_8 WHC;MY;QFK;DN;EIP;RS;TGV;LA A4_9 WH;CM;YQF;KD;NE;IP;RST;GV;LA
A4_10 WH;CM;YQ;FK;DN;EI;PR;ST;GV;LA   
A5_2 DSQPVLECWA;HFINMTYKGR A5_3 DSQPVLE;CWAHFI;NMTYKGR
A5_4 DSQPV;LECWA;HFINM;TYKGR A5_5 DSQP;VLEC;WAHF;INMT;YKGR
A5_6 DSQ;PVLE;CWA;HFI;NMTY;KGR A5_7 DSQ;PVL;ECW;AH;FIN;MTY;KGR
A5_8 DSQ;PV;LEC;WA;HFI;NM;TYK;GR A5_9 DS;QP;VLE;CW;AH;FI;NMT;YK;GR
A5_10 DS;QP;VL;EC;WA;HF;IN;MT;YK;GR   
  1. The 52 reduced-state amino acid alphabets. Each state is defined as a group of characters followed by a semi-colon, so for example, 'KRDEH' and 'ACFGILMNPQSTVWY' are reduced to the charged and uncharged states, respectively, in the CHARGE_HIS_2 alphabet.