AB Percent ID

--percent_id, -pi

Implemented in version 1.3

Description

Generate an all-by-all matrix of percent IDs among all the sequences in each alignment (if multiple alignments are present, then separate matrices will calculated for each one). The values are calculated by dividing the number of residues with a perfect match by the length of the alignment; note that gaps are considered mismatches, and are included in the overall value.

Examples

Input file: Ctenophores.nex

#NEXUS
begin data;
	dimensions ntax=5 nchar=78;
	format datatype=protein missing=? gap=-;
matrix
'Ate-PanxβG' MVAVATDLKELLVIKGKSRIDTFSDQYNRIFIVRLLMVCTIIMGFSWYTDSISCIVPETHNLD---GDFVSAACWIQG
'Hvu-PanxβE' MSIITGNLKSLLTIKFKPRHDTFTDQFNRIFMVKMAMVASFLLGLNWFKDTITCIVPASAGID---KGYVAQGCWIQG
'Ccr-PanxγA' M---------------------------RKALPLCLLFVTGMIFYKYNDEKLSCMKYSGDDPV--PDEFYHGYCWAKG
'Che-PanxβD' M--APPDIKKLLRIKIKPRKDPYTDQFSRIFMVKMMMLTATITGLSWAKDKFTCIVPKNHETT---AAFVQKACWING
'Nbi-PanxβG' MAGVTGDIKSLFNYKYKKRDDELSDQYSRIFMPKVMLIAAFLTGMSWYSDEIACLNPHKSLVGESIAKYSGKACWVNG
;
end;

Usage example 1

$: alb Ctenophores.nex -pi

Output

### Alignment 1 ###
	Ate-PanxβG	Hvu-PanxβE	Ccr-PanxγA	Che-PanxβD	Nbi-PanxβG
Ate-PanxβG		0.48	0.132	0.453	0.359
Hvu-PanxβE	0.48		0.079	0.493	0.385
Ccr-PanxγA	0.132	0.079		0.108	0.103
Che-PanxβD	0.453	0.493	0.108		0.423
Nbi-PanxβG	0.359	0.385	0.103	0.423

Input file: Panxs.phy

 4 481
Ate-PanxβG 
MVAVATDLKELLVIKGKSRIDTFSDQYNRIFIVRLLMVCTIIMGFSWYTDSISCIVPETHNLD---GDFVSAACWIQGVYVFKELTSRVDK---VAYFGMPKNIDFEGIEIGT------DNLCNLKPKLNEKKSENCIPMTKIFYLQYQYMPFFVAALAILYYLPYIAFRTLNKDKQSLKDEMKKD---DKTAKSIVENHFRNFEEARTTETR-NMTIRIILNIVIKVLYILSNVVALLALNNVLNDEFLSYGQKFVAWTRNNNTIQYDY--MGMRDLPKPGNALLPPFGYCEMYESARDVKTTLANAHKFV--CEISQNILYQYCLAVLWFAIVAGIVISVFGLLHCLIIYF---------IDFAGFRF--PKEEADFSRLHVREVELMHYVKEKDVKTFYECIQMLPKRDGDRE---KHNTLDG-------------------------------------------------------
Ate-PanxβD 
MASQINSIKSLLTIKPKSRNDDYTDQFHRIFMVKMSMVASLLLGLNWVKDTITCIIPGTAGIS---GDYVHQACWIQGFYIYRDLQHTPGK---FGLFGIPDDIENNGLHATS------GTPCHVNKH-----SVDCVPLTKTFYLQYQWFPFYMATLGFLYYLPYLLFRCVNADLISLKGNLKT----DVDIDVVVKNYF----NHVINPIG-KMRLRLIANIFVKLFYIIVNVIAFTGTDRLINGDFKNYGRDWMAWTKHDNKEEFDY--TETRKTWRPAEKLLPTFGLCEVLELGKDIKHSLFNSHRFV--CEISQNVLYQYVLALLWFLFIIGMVVSVLGLLMLIGEHVAIH------AVAVTSYDDADQTKKVYAALSLRECQYLECIRKKDIIVFTNVIRKLKDERLHLD---GNVYLS----NNIS-SISKN------QNPYQDSQM-------MLQETLNIS-----------
Hvu-PanxβI 
MIGLESDLRRILTVTLKARHDDLTDQLNRLIMVKLFLVCCLIMGISWFTDSINCIVPAINTVE---TAFVSQACWIQGFYVFKPLMTRFD----VAFFGIPRDIDSNGLLAS-------GELCTVQPSFGIA-SDKCIPMEKIFYLQYQWMPFLIGSLSAVYYIPYVFFLQANSDMISLKAAVMGK----EKPSKIVSMFF----GCKSQR---FLKLRVVSSIFVKSLYLIVNIGTFVFLNFLLNGEYYKYGVRWANWSKQSNTDAFDY--MGKKTNPRPGSQLLPPFGYCELFESSKDIKYTVANRHKFV--CELSQHVLYQYCLLVLWFFIIGGIIISSLGIFFHVYQYV---------HLICARYSYKGHKNMFLKTLTLRELLYLDLIKTKNNKLYEEVIENLELQSSI-----------------------------------------------LFEDNKCKKKRIGRKSLLRM
Che-PanxβF 
M-VVVRSLKDILALKIKARHDSPCDQFSRLFMTKMFLIAAVIMGFDYFSDRISCIHPKKTDLT---KEFIHAACWISGFYVYKEMRDRPRE---SGYYGIPYKIDHDGIDTQT------QQLCLTNNVKVF--RPECQSMTRIYYLQYQWMPFYIGALGVLYYLPYILFRIINVDLISLKSVLKSV---TSDADHIVRNYF----NYKINSIS-KLRMRVVLNLFVKCLYIVVNLFGFYFTDYLLHGNYRSYGTEYVRWARSDSARSHLP--IKFRKGPKPGNHLLPTMGYCEVEEASKDQLTVHHNSYVFL--CEISTNILYQYVLVVLWFLFIISICISIIGLLSALFGHL---------FKLTCYSR-SSPKKTIYRVITLREAEYLNFIKTKNMVMYGEVLRKLKQQRSDLQ---------------------GKIIDGFETS---------NGFV---------------------
 2 683
Mle-Panxα9 
----mldilskf------------kgvtpfkgitiddgwdqlnrsfmfvllvvmgttvtvr-qytgsvisc--------dgfkkfg--stfaedycwtqglytvlegydqp-sqnip---------ypgl---lpdeappct--------p-vrlkdgtrlkcpdpdqllsptrishlwyqwvpfyfwlaaaaffmpyllyknf-gmgdikplvrllhn--pves--dqelkkmtdkaatwlfykfd-lymseqsllasltrkhglglsmvfvkilyaavsfgcflltaemfsigd--fktygsew----ikklkl-ednlateekdklfpkmvacevkrwgasgieeeqgmcvlapnvinqylflilwfclvfvmfcnivsifaslikllftygsyrrllsta-flrddsa---ikhmyfnvgssgrlilhvlanntaprvfedilltlapkliqrkl-rgngkal------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Mle-Panxα6 
-m--lleilanf------------kgatpfkeivlddkwdqinrcymfllcvifgtvvtfr-qytggiiac--------dgltkfs--aafaedycwtqglytikeaydiv-dnslp---------ypgl---lpedappcl--------s-rrlvsggriecppadlyleptrvhhtwyqwipfyfwvisiafigpyivykql-gvnelkpilamlhn--pvdg--ddvtkdqiskvsrwlaikln-ifiqekstyakitqshrmfilifltkifylgvslatmyftdtmfesgr--yltygsew----fasldk-qsnytsfvrdrlfpkmvaceikrwgpsgmeeeqgmcvlapnvmnqylflifwfalvftifsntfsiffsvsthcfidggyqrfiqsc-flkensk---lkfiyfncgttgrtylhliaknvnprifeqliiklsadlveekn-kqhlkgskd------------------------------------------------------------------------------------------------------ilv-------------------------------------------------------------------------------------------------------------

Usage example 2

$: alb Panxs.phy -pi

Output

### Alignment 1 ###
	Ate-PanxβG	Ate-PanxβD	Hvu-PanxβI	Che-PanxβF
Ate-PanxβG		0.344	0.382	0.351
Ate-PanxβD	0.344		0.34	0.37
Hvu-PanxβI	0.382	0.34		0.351
Che-PanxβF	0.351	0.37	0.351

### Alignment 2 ###
	Mle-Panxα9	Mle-Panxα6
Mle-Panxα9		0.493
Mle-Panxα6	0.493