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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.