/usr/lib/R/site-library/Biostrings/extdata/Phylip.txt is in r-bioc-biostrings 2.42.1-1.
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Mask 1111111111 1111111111 1111111111 0011111111 1111111111
hprt_rhoca YVID-QMISA KAIAARVEAL GAEITEAFKD T-LVVVGLLR GSFVFIADLI
hprt_haein HHVD-VLISE NDVHARIAEL GAQITKFYQE KQLVVVGLLR GSFMFMADIV
hprt_haein HHVD-VLISE NDVHARIAEL GAQITKFYQE KQLVVVGLLR GSFMFMADIV
hprt_vibha HTVE-VMISE QEVQERIREL GKQITERYQG SELVMVGLLR GSFVFMADLA
hprt_ecoli HTVE-VMIPE AEIKARIAEL GRQITERYKD SGMVLVGLLR GSFMFMADLC
hprt_merun EDLEKVFIPH GLIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_monke EDLERVFIPH GLIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_human EDLERVFIPH GLIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_rat EDLEKVFIPH GLIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_mouse EDLEKVFIPH GLIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_crigr EDLEKVFIPH GVIMDRTERL ARDVMKEMGG HHIVALCVLK GGYKFFADLL
hprt_plafk KYLTKVLVPN GVIKNRIEKL AYDIKKVYNN EEFHILCLLK GSRGFFTALL
hprt_plafg KYLTKVLVPN GVIKNRIEKL AYDIKKVYNN EEFHILCLLK GSRGFFTALL
hgxr_toxog PYIDKILLPG GLVKDRVEKL AYDIHRTYFG EELHIICILK GSRGFFNLLI
hprt_schma ECLDYVLIPN GMIKDRLEKM SMDIVDYYEA CNITLMCVLK GGFKFLADLV
gprt_giard DVLESLLATF EECKALAADT ARRMNEYYKD --VTLVALLT GAYLYASLLT
hprt_trybb DFATSVLFTE AELHTRMRGV AQRIADDYSN CNLVIVSVLK GSFVFTADMV
hprt_tcruz EFAEKILFTE EEIRTRIMEV AKRIADDYKG KGLVLISVLK GSFMFTADLC
hprt_leido PMSAHTLVTQ EQVWAATAKC AKKIAEDYRS FKLYLLCVLK GSFIFTADLA
hprt_crifa PMSCRTLATQ EQIWSATAKC AKQIAEDYKQ YNLYLLCVLK GSFMFTADLA
hgxr_trifp DDLERVLYNQ DDIQKRIREL AAELTEFYED K-PVMICVLT GAVFFYTDLL
hprt_lacla KAIEKVLVSE EEIIEKSKEL GEILTKEYEG K-PLVLGILR GSVPFLAELI
hprt_bacsu HDIEKVLISE EEIQKKVKEL GAELTSEYQD T-PLAIGVLK GALPFMADLI
hprt_mycge MGIKSIVINE QQIEEGCQKA VNWCNAKFNN KKVIVLGILK GCIPFLGKVI
0000000000 0011111111 1111111100 1111111111 1110111111
R---EIGVPC EVDFLEASSY GNETTSTREV RVLKDLRGII GGR-DVLVVE
R---QINLPV EIEFMTTSSY GTGMTTNHDV RITKDLDGDI KGK-HVLIVE
R---QINLPV EIEFMTTSSY GTGMTTNHDV RITKDLDGDI KGK-HVLIVE
R---AIELTH QVDFMTASSY GNTMESSRDV RILKDLDDDI KGK-DVLIVE
R---EVQVSH EVDFMTASSY GSGMSTTRDV KILKDLDEDI RGK-DVLIVE
DYIKSLNRNT DRDFIRLKSY CNDQSTGDIK VIGGDDLSAL TGK-NVLIVE
DYIKALNRNS DRDFIRLKSY CNDQSTGDIK VIGGDDLSTL TGK-NVLIVE
DYIKALNRNS DRDFIRLKSY CNDQSTGDIK VIGGDDLSTL TGK-NVLIVE
DYIKALNRNS DRDFIRLKSY CNDQSTGDIK VIGGDDLSTL TGK-NVLIVE
DYIKALNRNS DRDFIRLKSY CNDQSTGDIK VIGGDDLSTL TGK-NVLIVE
DYIKALNRNS DRDFIRLKSY CNDQSTGDIK VIGGDDLSTL TGK-NVLIVE
KHLSRIHNYS AVHYVRVKSY CNDQSTGTLE IVS-EDLSCL KGK-HVLIVE
KHLSRIHNYS AVHYVRVKSY CNDQSTGTLE IVS-EDLSCL KGK-HVLIVE
DYLATIQKYS GRHYVRLKSY QNDNSTGQLT VLS-DDLSIF RDK-HVLIVE
DGLERTVRAR GIEFVRVKSY VNDVSIHEPI LTGLGDPSEY KDK-NVLVVE
VHLT------ --HFVKVSSY KGTRQES--V VFDEEDLKQL KEKREVVLID
RILGDFGVPT RVEFLRASSY GHDTKSCGRV DVKADGLCDI RGK-HVLVLE
RALSDFNVPV RMEFICVSSY GEGVTSSGQV RMLLDTRHSI EGH-HVLIVE
RFLADEGVPV KVEFICASSY GTGVETSGQV RMLLDVRDSV ENR-HILIVE
RFLCDEGVPV RIEFICASSY GTDVKTSGEV RLLLDVRDPV ENR-HLLIVE
K---HLDFQL EPDYIICSSY -SGTKSTGNL TISKDLKTNI EGR-HVLVVE
K---HIDCHL ETDFMTVSSY HGGTKSSGEV KLILDVDTAV KGR-DILIVE
K---HIDTYL EMDFMDVSSY GNSTVSSGEV KIIKDLDTSV EGR-DILIIE
---SKFSFDL QLDFMAVASY HGSHVQKQPP KIVLDMSHDP KDK-DILLIE
1111111111 0000000000 0000000000 0000000000 0000000000
DIIDTGHTIS KVMEMLRARA PRR--IECCA MLDKP-SRRE VDVKARWTGF
DIIDTGYTLE KVRDILNLRE PAS--LTICT LLDKP-SRRE VEVPVEWVGF
DIIDTGYTLE KVRDILNLRE PAS--LTICT LLDKP-SRRE VEVPVEWVGF
DIIDTGNTLN KIREILSLRE PKS--IAICT LLDKP-SRRE VEVPVDYVGF
DIIDSGNTLS KVREILSLRE PKS--LAICT LLDKP-SRRE VNVPVEFIGF
DIIDTGKTMQ TLLSLVQKYS PKM--VKVAS LLVKR-TPRS VGYRPDFVGF
DIIDTGKTMQ TLLSLVRQYN PKM--VKVAS LLVKR-TPRS VGYKPDFVGF
DIIDTGKTMQ TLLSLVRQYN PKM--VKVAS LLVKR-TPRS VGYKPDFVGF
DIIDTGKTMQ TLLSLVKQYS PKM--VKVAS LLVKR-TSRS VGYRPDFVGF
DIIDTGKTMQ TLLSLVKQYS PKM--VKVAS LLVKR-TSRS VGYRPDFVGF
DIIDTGKTMQ TLLSLVKRYN LKM--VKVAS LLVKR-TSRS VGYRPDFVGF
DIIDTGKTLV KFCEYLKKFE IKT--VAIAC LFIKR-TPLW NGFKADFVGF
DIIDTGKTLV KFCEYLKKFE IKT--VAIAC LFIKR-TPLW NGFKADFVGF
DIVDTGFTLT EFGERLKAVG PKS--MRIAT LVEKR-TDRS NSLKGDFVGF
DIIDTGKTIT KLISHLDSLS TKS--VKVAS LLVKR-TSPR NDYRPD-VGF
EYVDSGHTIF SIQEQIKHAK ICSCFVKDVD AIKKHSALAD TKMFYGYTPM
DILDTALTLR EVVDSLKKSE PAS--IKTLV AIDKP-GGRK IPFTAEYVVA
DIVDTALTLN YLYHMYFTRR PAS--LKTVV LLDKR-EGRR VPFSADYVVA
DIVDSAITLQ YLMRFMLAKK PAS--LKTVV LLDKP-SGRK VEVLVDYPVI
DIVDSAITLE YLKRFLQAKQ PAS--LKTVV LLDKP-SGRK VTLSVDYPVI
DIIDTGLTMY QLLNNLQMRK PAS--LKVCT LCDKDIGKKA YDVPIDYCGF
DIIDTGRTLK YLKELLEHRG AN---VKIVT LLDKP-EGRI VEIKPDYSGF
DIIDSGLTLS YLVELFRYRK AKS--IKIVT LLDKP-SGRK ADIKADFVGF
DIVDSGRSIK LVIDLLKTRH AKS--ITLIS LIEK-IKPKA FDINIDFSCF
0000011111 1111111111 1111111111 1
EIPDEFVVGY GLDYAQNHRN LPFIGTVRFT D
EIPDEFVVGY GIDYAQRHRN LGYIGKVVLE E
EIPDEFVVGY GIDYAQRHRN LGYIGKVVLE E
AIPDEFVVGV GIDYAQKYRD LPFIGKVVPQ E
SIPDEFVVGY GIDYAQRYRH LPYIGKVILL D
EIPDKFVVGY ALDYNEYFRD LNHVCVISES G
EIPDKFVVGY ALDYNEYFRD LNHVCVISET G
EIPDKFVVGY ALDYNEYFRD LNHVCVISET G
EIPDKFVVGY ALDYNEHFRD LNHVCVISES G
EIPDKFVVGY ALDYNEYFRD LNHVCVISET G
EIPDKFVVGY ALDYNEYFRD LNHICVISET G
SIPDHFVVGY SLDYNEIFRD LDHCCLVNDE G
SIPDHFVVGY SLDYNEIFRD LDHCCLVNDE G
SIEDVWIVGC CYDFNEMFRD FDHVAVLSDA A
EVPNRFVVGY ALDYNDNFRD LHHICVINEV G
P-KGSWLIGF GLDDNGLRRG WAHLFDINLS E
DVPNVFVVGY GLDYDQSYRE VRDVVILKPS V
NIPNAFVIGY GLDYDDTYRE LRDIVVLRPE V
TIPHAFVIGY GMDYAESYRE LRDICVLKKE Y
TIPHAFVIGY GMDFAEAYRE LRDVCVLKKE Y
VVENRYIIGY GFDFHNKYRN LPVIGILKES V
TIPNEFVVGF GLDYEENYRN LPYVGVLKPE V
EVPDAFVVGY GLDYAERYRN LPYIGVLKPA V
KVKDNFLVGF GLDYDGFYRN LPYVGVFEPD N
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