#NEXUS
[! ]
[! ************************************************************************************** ]
[! Supplementary File S4: Avian ATP5F1A sequence alignment                                ]
[!                                                                                        ]
[! This is a nexus format file. If you execute the file in PAUP it will begin logging     ]
[! to ATP5F1A_branch_lengths.log.txt and estimate branch lengths using the parsimony      ]
[! criterion. You may wish to rename the file ATP5F1A_mafft_annotated.nex, if you do this ]
[! modify the gettrees command in the PAUP block (see comment in PAUP block)              ]
[!                                                                                        ]
[! These data are amino acid sequences extracted from high-quality genome assemblies      ]
[!   - aligned by mafft version 7, online server                                          ]
[!   - minor modification to alignment at N-term of Oxyura_jamaicensis_Un, appears to be  ]
[!     incorrect annotation                                                               ]
[!   - redundant isoforms (TAXSET "isoforms_delete") and gaps associated with an N-term   ]
[!     rusticolus W (CHARSET "F_rusticolus_ext") are excluded if this file is executed in ]
[!     PAUP. Analyses were conducted after deleting/excluding these data                  ]
[!   - functionally important sites based on homology to uniprot P25705 are included as   ]
[!     comments. They can be found by searching for "P25705" in a text editor             ]
[!                                                                                        ]
[! Functional residues, based on homology with uniprot P25705 (the human ATP5F1A protein) ]
[! are presented as comments embedded in the alignment.                                   ]
[! ************************************************************************************** ]
[! ]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=29;
	TAXLABELS
		Meleagris_gallopavo_Z Gallus_gallus_Z Gallus_gallus_W_X2 Gallus_gallus_W_X1 Cygnus_olor_W_hit1 Gallus_gallus_W_X3 Aythya_fuligula_Z Cygnus_olor_Z Oxyura_jamaicensis_Z Oxyura_jamaicensis_Un Aythya_fuligula_W Cygnus_olor_W_hit2_X2 Cygnus_olor_W_hit2_X1 Chiroxiphia_lanceolata_W Molothrus_ater_Un_W Taeniopygia_guttata_W Hirundo_rustica_W Taeniopygia_guttata_Z Molothrus_ater_Z Chiroxiphia_lanceolata_Z Hirundo_rustica_Z Melopsittacus_undulatus_Z Strigops_habroptila_Z Melopsittacus_undulatus_W_pseudogene Strigops_habroptila_W Falco_rusticolus_Z Falco_naumanni_Z Falco_rusticolus_W Falco_naumanni_W 
	;

END;


BEGIN CHARACTERS;
	DIMENSIONS  NCHAR=633;
	FORMAT DATATYPE = Protein INTERLEAVE GAP = - MISSING = ?;
	MATRIX
	Meleagris_gallopavo_Z                 ----------------------------------------------------------------------------------------------------
	Gallus_gallus_Z                       -----------------------------------------------------------------------------MLSARVAAVLARSLPRQAGLVSR
	Gallus_gallus_W_X2                    -----------------------------------------------------------------------------MFSARVAAAFARSVPRQGGLISR
	Gallus_gallus_W_X1                    -----------------------------------------------------------------------------MFSARVAAAFARSVPRQGGLISR
	Cygnus_olor_W_hit1                    -----------------------------------------------------------------------------MLSAHLAVTLARSLPRHAGLVSR
	Gallus_gallus_W_X3                    -----------------------------------------------------------------------------MFSARVAAAFARSVPRQGGLISR
	Aythya_fuligula_Z                     -----------------------------------------------------------------------------MLSARLAATLARSLPRHAGLVSR
	Cygnus_olor_Z                         -----------------------------------------------------------------------------MLSARLAATLARSLPRHAGLVSR
	Oxyura_jamaicensis_Z                  -----------------------------------------------------------------------------MLSARLAATLARSLPRHAGLVSR
	Oxyura_jamaicensis_Un                 --------------------------------------------------------------------AKSVLKYLL-----------------------
	Aythya_fuligula_W                     -----------------------------------------------------------------------------MFSTRLAGTVAHSLMRYASLVSR
	Cygnus_olor_W_hit2_X2                 -----------------------------------------------------------------------------MLSARLAATLARSLPRYAGLISR
	Cygnus_olor_W_hit2_X1                 -----------------------------------------------------------------------------MLSARLAATLARSLPRYAGLISR
	Chiroxiphia_lanceolata_W              ----------------------------------------------------------------------------------------------------
	Molothrus_ater_Un_W                   -----------------------------------------------------------------------------MFSTSVAASLARSLPRQAGLISR
	Taeniopygia_guttata_W                 -----------------------------------------------------------------------------MFSARVAASLARSLPWQAGLISR
	Hirundo_rustica_W                     -----------------------------------------------------------------------------MFSARLSASVARSLPRQASLISR
	Taeniopygia_guttata_Z                 -----------------------------------------------------------------------------MLSARVAATLARSLPRQAGLVSR
	Molothrus_ater_Z                      -----------------------------------------------------------------------------MLSARVAAALARSLPRQAGLVSR
	Chiroxiphia_lanceolata_Z              -----------------------------------------------------------------------------MLSARVAAALARSLPRQAGLVSR
	Hirundo_rustica_Z                     -----------------------------------------------------------------------------MLSARVAAALARSLPRQAGLVSR
	Melopsittacus_undulatus_Z             ----------------------------------------------------------------------------MMLSARVAAALSRSLPRQAGLVSR
	Strigops_habroptila_Z                 ----------------------------------------------------------------------------MMLSARVAAALARSLPRQAGLVSR
	Melopsittacus_undulatus_W_pseudogene  -----------------------------------------------------------------------------MFITRVAAALAYSLPQQASLISR
	Strigops_habroptila_W                 -----------------------------------------------------------------------------MLAARVIAALARSLPQQASLISR
	Falco_rusticolus_Z                    -----------------------------------------------------------------------------MLSARVAAALARSLPRQAGLISR
	Falco_naumanni_Z                      -----------------------------------------------------------------------------MLSARVAAALARSLPRQAGLISR
	Falco_rusticolus_W                    MYRNILAQGRRAGKGGTTSEGSREKHFRVSPRPAGVVLAAKRGGVRCCHFVERVWYWQPPPFSLKSSLEEPSVTAAAMLSARVVAALARSLPQQAGLNSR
	Falco_naumanni_W                      -----------------------------------------------------------------------------MLSARVVAALARSLPQQAGLDSR


	Meleagris_gallopavo_Z                 -----------------MGFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Gallus_gallus_Z                       NALGAAFVATRNIHASKMRFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFFFGLKGMSLNLEPDNVGVVVFGNDR
	Gallus_gallus_W_X2                    NTLCVASVAARNIHASKTHFQRTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Gallus_gallus_W_X1                    NTLCVASVAARNIHASKTHFQRTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Cygnus_olor_W_hit1                    NTLGAAFVATRSIHASKTHFQKTDTAEVSSILEERILGADTSAKLEEIGRVLSIGDGIAPVYGLRNVQAEEMVEFSSGLKGTFLNLEPDNVGVVVFGNDR
	Gallus_gallus_W_X3                    NTLCVASVAARNIHASKTHFQRTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Aythya_fuligula_Z                     NTLGAAFVATRNIHASKNHFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Cygnus_olor_Z                         NTLGAAFVATRNIHASKTHFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Oxyura_jamaicensis_Z                  NTLGAAFVATRNIHASKTHFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Oxyura_jamaicensis_Un                 -----------------------GTAEVSSILEERILGADTSAELEETGHVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Aythya_fuligula_W                     NTLGAAVVATRNVHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Cygnus_olor_W_hit2_X2                 NTLGAAFVATRNIHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Cygnus_olor_W_hit2_X1                 NTLGAAFVATRNIHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Chiroxiphia_lanceolata_W              -----------------MCFQKTGSVEVSSILEEHILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Molothrus_ater_Un_W                   NTLGAAFVATRNLHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Taeniopygia_guttata_W                 NTLGAVFVATRNLHAFKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Hirundo_rustica_W                     NTLGAAFVATRNLHASKTSFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Taeniopygia_guttata_Z                 STLPAAFVATRNLHASKPRFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Molothrus_ater_Z                      NTLGAAFVATRNLHASKACFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Chiroxiphia_lanceolata_Z              NTLGAAFVATRNLHASKPCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Hirundo_rustica_Z                     NTLSAAFVATRNLHASKPCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Melopsittacus_undulatus_Z             NTLGAAFVATRNLHASKTCCQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Strigops_habroptila_Z                 NTLGAAFLATRNIHASKTCYQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Melopsittacus_undulatus_W_pseudogene  HILGAVFVATRNIHASKACFQKTGTAEVSSILEEHILGTDTSAELEETGHVFSIVDGIACVYGLRNVQAE-MVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Strigops_habroptila_W                 HTLGAVFVATRNIHASKACFQKTGTAEVSSVLEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Falco_rusticolus_Z                    NTLGAAFVATRNIHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Falco_naumanni_Z                      NTLGAAFVATRNIHASKTCFQKTGTAEVSSILEERILGADTAAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Falco_rusticolus_W                    NTLGAAFVATRNIHASKTCFQKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR
	Falco_naumanni_W                      NTLGAAFVATRNIHASKTCFEKTGTAEVSSILEERILGADTSAELEETGRVLSIGDGIARVYGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDR

[ Nucleotide binding based on homology to uniprot P25705 213-220                                                                   DRQTGKTS - present in all]
	Meleagris_gallopavo_Z                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Gallus_gallus_Z                       LIKEGDVVKRTGAIVDVPVGEELLGRVVVALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Gallus_gallus_W_X2                    LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKSSFTSKSRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Gallus_gallus_W_X1                    LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKSSFTSKSRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Cygnus_olor_W_hit1                    LIKEGDIVKRTGATVDIPVGEELLGRVVDALGNPIDGKGPITSKTSRRVGLKAPGIIPRISVREPMQTGIKAVDSLMPIGRGRRELIIGDRQTGKTSIAI
	Gallus_gallus_W_X3                    LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKSSFTSKSRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Aythya_fuligula_Z                     LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Cygnus_olor_Z                         LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Oxyura_jamaicensis_Z                  LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Oxyura_jamaicensis_Un                 LIREGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITLKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Aythya_fuligula_W                     LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Cygnus_olor_W_hit2_X2                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Cygnus_olor_W_hit2_X1                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Chiroxiphia_lanceolata_W              LIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSIAPKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Molothrus_ater_Un_W                   LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSVASKMRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Taeniopygia_guttata_W                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSIASKMRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Hirundo_rustica_W                     LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Taeniopygia_guttata_Z                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGAIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Molothrus_ater_Z                      LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGAIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Chiroxiphia_lanceolata_Z              LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGAIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Hirundo_rustica_Z                     LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGAIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Melopsittacus_undulatus_Z             LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSIASKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Strigops_habroptila_Z                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGSIASKSRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Melopsittacus_undulatus_W_pseudogene  LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQHELIIGDRQTGKTSIAI
	Strigops_habroptila_W                 LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Falco_rusticolus_Z                    LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Falco_naumanni_Z                      LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Falco_rusticolus_W                    LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKMRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI
	Falco_naumanni_W                      LIKEGDVVKRTGAIVDVPVGEELLGRVVDALGNPIDGKGPVTSKMRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAI


	Meleagris_gallopavo_Z                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Gallus_gallus_Z                       DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Gallus_gallus_W_X2                    DTIINQKRFNDGADEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Gallus_gallus_W_X1                    DTIINQKRFNDGADEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Cygnus_olor_W_hit1                    DTIINQKQFNDGTDEKKQLYCIYVAIGQKRSTVAQLVKRLTDAD--TMKYTIVVSATASDAAPLPYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Gallus_gallus_W_X3                    DTIINQKRFNDGADEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Aythya_fuligula_Z                     DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Cygnus_olor_Z                         DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Oxyura_jamaicensis_Z                  DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Oxyura_jamaicensis_Un                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDSGKHALIIYDDLSKQAVAY
	Aythya_fuligula_W                     DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDSGKHALIIYDDLSKQAVAY
	Cygnus_olor_W_hit2_X2                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDSGKHALIIYDDLSKQAVAY
	Cygnus_olor_W_hit2_X1                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDSGKHALIIYDDLSKQAVAY
	Chiroxiphia_lanceolata_W              DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Molothrus_ater_Un_W                   DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Taeniopygia_guttata_W                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Hirundo_rustica_W                     DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Taeniopygia_guttata_Z                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Molothrus_ater_Z                      DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Chiroxiphia_lanceolata_Z              DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Hirundo_rustica_Z                     DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Melopsittacus_undulatus_Z             DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Strigops_habroptila_Z                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Melopsittacus_undulatus_W_pseudogene  DTINNQK-FNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDTDTNAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNRKHALIIYDDLSKQAVAY
	Strigops_habroptila_W                 DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Falco_rusticolus_Z                    DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Falco_naumanni_Z                      DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Falco_rusticolus_W                    DTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY
	Falco_naumanni_W                      DTVINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAD--AMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAY

[ Site required for activity based on annotation to uniprot P25705 413                                                               S - present in all except Gallus W isoform X2 ]
	Meleagris_gallopavo_Z                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Gallus_gallus_Z                       RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Gallus_gallus_W_X2                    RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDG------------------------------
	Gallus_gallus_W_X1                    RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Cygnus_olor_W_hit1                    RQMSLLLHRPPGREAYPGDVFYLHSRLLGRAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNIISITDGQIFLETELFYKGIRPAINIGLSVSRVGSAA
	Gallus_gallus_W_X3                    RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Aythya_fuligula_Z                     RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Cygnus_olor_Z                         RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Oxyura_jamaicensis_Z                  RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Oxyura_jamaicensis_Un                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Aythya_fuligula_W                     RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Cygnus_olor_W_hit2_X2                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Cygnus_olor_W_hit2_X1                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Chiroxiphia_lanceolata_W              RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Molothrus_ater_Un_W                   RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Taeniopygia_guttata_W                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Hirundo_rustica_W                     RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Taeniopygia_guttata_Z                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Molothrus_ater_Z                      RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Chiroxiphia_lanceolata_Z              RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Hirundo_rustica_Z                     RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Melopsittacus_undulatus_Z             RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Strigops_habroptila_Z                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Melopsittacus_undulatus_W_pseudogene  RQMSLLL-HPPGREA-SGDVFYLHSHLLERAAKMNESFGGGSLTTLPVTETQAGDVSAYIPINVISITDGQIFLETELFYKGVRPAINVGLSVSRVGSAA
	Strigops_habroptila_W                 RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Falco_rusticolus_Z                    RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Falco_naumanni_Z                      RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Falco_rusticolus_W                    RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDTFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA
	Falco_naumanni_W                      RQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAA

[ Nucleotide binding based on homology to uniprot P25705 473-475                             QGQ - note: not present in Cygnus_olor_W_hit1 ]
	Meleagris_gallopavo_Z                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Gallus_gallus_Z                       QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Gallus_gallus_W_X2                    ------QVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHEA
	Gallus_gallus_W_X1                    QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHEA
	Cygnus_olor_W_hit1                    QTRAMKQVAGIMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKRGQYVPTAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Gallus_gallus_W_X3                    QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYDVSGKTHRAVVLWCATATRWLKAENSI----------------QP
	Aythya_fuligula_Z                     QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Cygnus_olor_Z                         QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Oxyura_jamaicensis_Z                  QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHILSQHQA
	Oxyura_jamaicensis_Un                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Aythya_fuligula_W                     QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQT
	Cygnus_olor_W_hit2_X2                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Cygnus_olor_W_hit2_X1                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Chiroxiphia_lanceolata_W              QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPNKITKFESAFLAHVLSQHQA
	Molothrus_ater_Un_W                   QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Taeniopygia_guttata_W                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Hirundo_rustica_W                     QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Taeniopygia_guttata_Z                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQD
	Molothrus_ater_Z                      QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQD
	Chiroxiphia_lanceolata_Z              QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Hirundo_rustica_Z                     QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Melopsittacus_undulatus_Z             QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Strigops_habroptila_Z                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Melopsittacus_undulatus_W_pseudogene  QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRDHLDKLEPSKITKFESAFIAHVLSHHQV
	Strigops_habroptila_W                 QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQV
	Falco_rusticolus_Z                    QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Falco_naumanni_Z                      QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Falco_rusticolus_W                    QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITKFESAFLAHVLSQHQA
	Falco_naumanni_W                      QTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYAGVRGHLDKLEPSKITRFESAFLAHVLSQHQA


	Meleagris_gallopavo_Z                 LLSTI-RTEGKISDQTEAKLKEIVTNFLSTF--
	Gallus_gallus_Z                       LLSTI-RTEGKISDQTEAKLKEIVTNFLSTFEA
	Gallus_gallus_W_X2                    LLSTI-RTEGKISDQTEAKLKEIVTNFLSTFEA
	Gallus_gallus_W_X1                    LLSTI-RTEGKISDQTEAKLKEIVTNFLSTFEA
	Cygnus_olor_W_hit1                    LLSTI-RTKGKISDQTEAKLKEIVTNFLSTFKA
	Gallus_gallus_W_X3                    L--------------------------------
	Aythya_fuligula_Z                     LLSTI-RTEGKISDQTEAKLKEIVTNFLSTFEA
	Cygnus_olor_Z                         LLSTI-RTEGKISDQTEAKLKEIVTNFLSTFEA
	Oxyura_jamaicensis_Z                  LLSTI-RTEGKISDQTEGKLKEIVTNFLSTFEA
	Oxyura_jamaicensis_Un                 LLSTL-RTEGKISDQTEAKLKEIVTNFLATFEA
	Aythya_fuligula_W                     LLSTI-RTEGKISDQTEVKLKEIVTNFLATFEA
	Cygnus_olor_W_hit2_X2                 LLSTI-RTEGKISDQTEAKLKEIVTNFLATFEA
	Cygnus_olor_W_hit2_X1                 LLSTISRTEGKISDQTEAKLKEIVTNFLATFEA
	Chiroxiphia_lanceolata_W              LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Molothrus_ater_Un_W                   LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Taeniopygia_guttata_W                 LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Hirundo_rustica_W                     LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Taeniopygia_guttata_Z                 LLSTI-RTEGKISDQTEAKLKEIVTKFLSTFEA
	Molothrus_ater_Z                      LLSTI-RTEGKISDQTEAKLKEIVTKFLSTFEA
	Chiroxiphia_lanceolata_Z              LLSTI-RTEGKISDQTEAKLKEIVTNFLATFEA
	Hirundo_rustica_Z                     LLSTI-RTEGKISDQTEAKLKEIVTNFLATFEA
	Melopsittacus_undulatus_Z             LLSTI-RTEGKISDQTEAKLKEIVTNFLATFEA
	Strigops_habroptila_Z                 LLSTI-RTEGKISDQTEAKLKEIVTNFLATFEA
	Melopsittacus_undulatus_W_pseudogene  LLSTI-RTEGKISDQTEAKLKEVVTSFLATFEA
	Strigops_habroptila_W                 LLSTI-RTEGKISDQTEAKLKEVVTSFLATFEA
	Falco_rusticolus_Z                    LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Falco_naumanni_Z                      LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Falco_rusticolus_W                    LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA
	Falco_naumanni_W                      LLSTI-RTEGKISDQTEAKLKEIVTSFLATFEA

;


END;

BEGIN SETS;
	CHARSET F_rusticolus_ext   =   1 -  77;
	TAXSET isoforms_delete = Gallus_gallus_W_X2 Gallus_gallus_W_X3 Cygnus_olor_W_hit2_X2;
	
	[ bur is residues with >0.5 site probability for the buried component of the XB model ] 
	CHARSET bur =  81 83 85 91 95 97 102 103 105 106 108 109 110 113 115 117 121 123 124 126 127 128 131 132 133 134 136 137 138 139 141 143 144 145 146 147 148 149 151 154 155 157 158 159 161 162 163 164 167 169 170 171 173 174 178 179 180 181 184 186 187 191 192 193 194 195 197 201 202 204 205 207 208 209 211 212 213 214 215 217 219 220 221 222 223 224 225 227 228 230 231 232 235 237 238 242 244 249 250 251 252 253 255 256 257 260 262 264 268 269 270 271 272 273 276 279 280 282 285 286 287 288 289 293 294 295 296 298 299 300 302 303 304 307 312 313 315 316 317 318 319 320 322 323 324 325 326 327 329 332 333 334 336 337 338 340 341 343 345 347 349 350 351 352 353 354 356 357 358 361 362 364 366 367 368 370 372 376 377 378 384 386 387 388 389 390 393 395 397 398 399 400 405 406 407 412 414 415 416 418 420 422 423 427 428 429 431 432 433 436 439 440 441 443 444 445 446 448 449 450 451 453 454 456 458 459 460 462 464 465 467 468 470 472 474 475 476 477 478 480 481 482 483 486 487 489 490 491 493 496 497 499 500 502 504 506 508 509 510 511 513 514 515 516 517 519 521 522 523 524 526 529 532 534 535 536 539 540 543 544 546 547 548 549 550 551 553 555 556 559 560 561 562 564 565 566 567 568 569 570 571 573 575 577 578 579 582 583 584 587 589 591 592 594 595 599 601 602 604 605 608 609 610 611 612 616 617 618 619 620 621 622 623 624 625 628 630 632 633 ;
END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  633;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  633;


END;

BEGIN PAUP;
	exclude F_rusticolus_ext ;
	delete isoforms_delete ;
	outgroup Meleagris_gallopavo_Z Gallus_gallus_Z Gallus_gallus_W_X2 Gallus_gallus_W_X1 Cygnus_olor_W_hit1 Gallus_gallus_W_X3 Aythya_fuligula_Z Cygnus_olor_Z Oxyura_jamaicensis_Z Oxyura_jamaicensis_Un Aythya_fuligula_W Cygnus_olor_W_hit2_X2 Cygnus_olor_W_hit2_X1 ;
END;

Begin trees;  
[! Four trees: ]
[!   - Both "species trees" conform to the likely species tree and assume the barriers to  ]
[!     recombination correspond to those in the intron tree. The trees are:                ]
[!   - species_tree1 = species tree with Cygnus_olor_W_hit1 united with Anseriformes Z     ]
[!   - species_tree2 = species tree with Cygnus_olor_W_hit1 united with Anseriformes W     ]
[!   - optimal       = tree estimated using MamXB+FO+G4                                    ]
[!   - opt_move_cygW = optimal tree with Cygnus_olor_W_hit1 united with Anseriformes W     ]
	tree species_tree1 = [&U] (Meleagris_gallopavo_Z,Gallus_gallus_Z,(Gallus_gallus_W_X1,(((((Cygnus_olor_W_hit1,Cygnus_olor_Z),Aythya_fuligula_Z),Oxyura_jamaicensis_Z),(Oxyura_jamaicensis_Un,(Aythya_fuligula_W,Cygnus_olor_W_hit2_X1))),((((Chiroxiphia_lanceolata_W,((Molothrus_ater_Un_W,Taeniopygia_guttata_W),Hirundo_rustica_W)),(((Taeniopygia_guttata_Z,Molothrus_ater_Z),Hirundo_rustica_Z),Chiroxiphia_lanceolata_Z)),((Melopsittacus_undulatus_Z,Strigops_habroptila_Z),(Melopsittacus_undulatus_W_pseudogene,Strigops_habroptila_W))),((Falco_rusticolus_Z,Falco_naumanni_Z),(Falco_rusticolus_W,Falco_naumanni_W))))));
	tree species_tree2 = [&U] (Meleagris_gallopavo_Z,Gallus_gallus_Z,(Gallus_gallus_W_X1,(((((Cygnus_olor_W_hit1,Cygnus_olor_W_hit2_X1),Aythya_fuligula_W),Oxyura_jamaicensis_Un),((Aythya_fuligula_Z,Cygnus_olor_Z),Oxyura_jamaicensis_Z)),((((Chiroxiphia_lanceolata_W,((Molothrus_ater_Un_W,Taeniopygia_guttata_W),Hirundo_rustica_W)),(((Taeniopygia_guttata_Z,Molothrus_ater_Z),Hirundo_rustica_Z),Chiroxiphia_lanceolata_Z)),((Melopsittacus_undulatus_Z,Strigops_habroptila_Z),(Melopsittacus_undulatus_W_pseudogene,Strigops_habroptila_W))),((Falco_rusticolus_Z,Falco_naumanni_Z),(Falco_rusticolus_W,Falco_naumanni_W))))));
	tree optimal       = [&U] (Meleagris_gallopavo_Z:0.0000027571,Gallus_gallus_Z:0.0100823416,(((Gallus_gallus_W_X1:0.0346872106,((((Chiroxiphia_lanceolata_W:0.0174935433,Hirundo_rustica_W:0.0099184470)42:0.0000022606,(Molothrus_ater_Un_W:0.0059001582,Taeniopygia_guttata_W:0.0059043683)68:0.0019594460)95:0.0076837954,(((Taeniopygia_guttata_Z:0.0097089384,Molothrus_ater_Z:0.0019069607)82:0.0058379594,(Chiroxiphia_lanceolata_Z:0.0000027571,Hirundo_rustica_Z:0.0019066009)70:0.0000027571)91:0.0038504529,Melopsittacus_undulatus_Z:0.0038060277)18:0.0000021305)63:0.0019208794,Strigops_habroptila_Z:0.0057495611)65:0.0020145912)38:0.0018300470,(((Melopsittacus_undulatus_W_pseudogene:0.0592210349,Strigops_habroptila_W:0.0052562615)97:0.0142282508,(Falco_rusticolus_W:0.0019016032,Falco_naumanni_W:0.0076597814)95:0.0039508478)88:0.0037008430,(Falco_rusticolus_Z:0.0000027571,Falco_naumanni_Z:0.0018893256)73:0.0000027571)92:0.0056434051)55:0.0000021595,((Cygnus_olor_W_hit1:0.0569840686,((Aythya_fuligula_Z:0.0019088998,Oxyura_jamaicensis_Z:0.0038065844)29:0.0000027571,Cygnus_olor_Z:0.0000027571)58:0.0000028033)89:0.0039042975,((Oxyura_jamaicensis_Un:0.0105813954,Cygnus_olor_W_hit2_X1:0.0000024554)42:0.0016687209,Aythya_fuligula_W:0.0225579938)90:0.0039417979)74:0.0057082904)87:0.0074582262);
	tree opt_move_cygW = [&U] (Meleagris_gallopavo_Z,Gallus_gallus_Z,(((Gallus_gallus_W_X1,((((Chiroxiphia_lanceolata_W,Hirundo_rustica_W),(Molothrus_ater_Un_W,Taeniopygia_guttata_W)),(((Taeniopygia_guttata_Z,Molothrus_ater_Z),(Chiroxiphia_lanceolata_Z,Hirundo_rustica_Z)),Melopsittacus_undulatus_Z)),Strigops_habroptila_Z)),(((Melopsittacus_undulatus_W_pseudogene,Strigops_habroptila_W),(Falco_rusticolus_W,Falco_naumanni_W)),(Falco_rusticolus_Z,Falco_naumanni_Z))),(((Aythya_fuligula_Z,Oxyura_jamaicensis_Z),Cygnus_olor_Z),((Oxyura_jamaicensis_Un,(Cygnus_olor_W_hit1,Cygnus_olor_W_hit2_X1)),Aythya_fuligula_W))));
End;

BEGIN PAUP;

	log file=ATP5F1A_branch_lengths.log.txt replace;
	
	[! ]
	[! Loading trees, tree 1 minimizes the number of recombination block given the species ]
	[! tree (with the intronless Cygnus_olor_W_hit1 placed within the Z gametologs)        ]
	gettrees file=Supplementary_File_S4.txt;  [ ATP5F1A_mafft_annotated.nex; if renamed ]
 
	[! ----------------------------------------------------------------------------------- ]
	[! ]
	[! Analyze complete ATP5F1A alignment. Calculate MP branch length estimates (ACCTRAN)  ]
	[! for sites where the contribution of the eXp mixture component of MamXB is higher    ]
	[! than the contribution of the Bur mixture component ("EXPOSED SITES") and vice versa ]
	[! ("BURIED SITES")                                                                    ]
	[! ]

	[! ]	
	[! ************************************************************* ]
	[! *** CALCULATE BRANCH LENGTHS FOR EXPOSED SITES (all taxa) *** ]
	[! ************************************************************* ]
	[! ]
	exclude bur;
	describetrees 1 / plot=phylogram brlens=yes;

	[! ]	
	[! ************************************************************* ]
	[! *** CALCULATE BRANCH LENGTHS FOR BURIED SITES (all taxa)  *** ]
	[! ************************************************************* ]
	[! ]
	include bur / only;
	describetrees 1 / plot=phylogram brlens=yes;
	
	[! ]
	[! ----------------------------------------------------------------------------------- ]
	[! ]
	[! Conduct the same analysis after deleting the pseudogenes.                           ]
	[! ]
	delete Cygnus_olor_W_hit1 Melopsittacus_undulatus_W_pseudogene / prune=yes ;
	exclude F_rusticolus_ext / only ;
	
	[! ]	
	[! ************************************************************************* ]
	[! *** CALCULATE BRANCH LENGTHS FOR EXPOSED SITES (pseudogenes excluded) *** ]
	[! ************************************************************************* ]
	[! ]
	exclude bur;
	describetrees 1 / plot=phylogram brlens=yes;

	[! ]	
	[! ************************************************************************* ]
	[! *** CALCULATE BRANCH LENGTHS FOR BURIED SITES (pseudogenes excluded)  *** ]
	[! ************************************************************************* ]
	[! ]
	include bur / only;
	describetrees 1 / plot=phylogram brlens=yes;

	log stop;
	
END;
