AB Order IDs

--order_ids, -oi

Description

Sort all sequences by ID in alpha-numeric order. AlignBuddy will do its best to rationally handle any numbers (including 0-padded numbers) that are present in the IDs.

Arguments

'rev' ( exact string )

Optional. Pass in the word 'rev' will reverse the sort order.

Examples

Input file: Drosophila.nex

#NEXUS
begin data;
    dimensions ntax=8 nchar=316;
    format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ3' -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ07' --L--SV----R-Q-RIDNIVFKLHYRWTVILLVA-TLLITSRQYIGEHIQCL--VVSPVINTFCFFTPTF-VD--P---PGI--D-RHAYYQWVPFVLFFQALCFYIPHALWKW-EGGRIKALVK--LG-MERVKD---IRDM--RLNWG-HVFAEVLNLINLLLQITWTNRFLGGQFLTLG------HALKN-RSDEVV---FPKITKCKFHKFGDSGSIQMHDALCVMALNIMNEKIYIILWFWYAFLLIVTVLGLLWRLCF---VR-WSL----------P-LASNWMFLFFLRSNLS-----E-L----DN
'Dme-Panxδ12' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'Dme-Panxδ5' MSAVKPLSKYLQFKIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-S-EEKNIESYCWTMGTYYNEASIAE--GVEIRQYLRYYQWVIILLLFQSFVFYFPSCLWKVWEGRRLKQLCEVDNTRRM--LVKYFDMHFC----YMAYVFCEVLNFLISVVNIIVLEVFLNGFWSKYLRALW-------DRWV-SV---FPKIAKCELKF-GGSGTANVMDNLCILPLNILNEKIFVFLWAWFL-LALMSGLNLLCRLAICSRLREQMIRTKRHVKRALDLTIGDWFLMMKVSVNVNPMLFRDLMQEL---
'Dme-Panxδ6' MAAVKPLSNYLRLKVRIYDPIFTLHSKCTIVILLTCTFLLSAKQYFGEPILCL-S-SERQADSYCWTMGTYWNEQSIAE--GVETRMYLRYYQWVFMILLFQSLLFYFPSFLWKVWEGQRMEQLCEVDRTRQM--LTRYFPIHWC----YSIYAFCELLNVFISILNFWLMDVVFNGFWYKYIHALW-------NLWM-RV---FPKVAKCEFVY-GPSGTPNIMDILCVLPLNILNEKIFAVLYVWFL-FALLAIMNILYRLLICCPLRLQLLNPKSHVREVLSAGYGDWFVLMCVSINVNPTLFRELLEQL--D
'Dme-Panxδ04' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ8' LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
;
end;

Usage example 1

$: alb Drosophila.nex -oi

Output

#NEXUS
begin data;
	dimensions ntax=8 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ1'  YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ3'  -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ04' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ5'  MSAVKPLSKYLQFKIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-S-EEKNIESYCWTMGTYYNEASIAE--GVEIRQYLRYYQWVIILLLFQSFVFYFPSCLWKVWEGRRLKQLCEVDNTRRM--LVKYFDMHFC----YMAYVFCEVLNFLISVVNIIVLEVFLNGFWSKYLRALW-------DRWV-SV---FPKIAKCELKF-GGSGTANVMDNLCILPLNILNEKIFVFLWAWFL-LALMSGLNLLCRLAICSRLREQMIRTKRHVKRALDLTIGDWFLMMKVSVNVNPMLFRDLMQEL---
'Dme-Panxδ6'  MAAVKPLSNYLRLKVRIYDPIFTLHSKCTIVILLTCTFLLSAKQYFGEPILCL-S-SERQADSYCWTMGTYWNEQSIAE--GVETRMYLRYYQWVFMILLFQSLLFYFPSFLWKVWEGQRMEQLCEVDRTRQM--LTRYFPIHWC----YSIYAFCELLNVFISILNFWLMDVVFNGFWYKYIHALW-------NLWM-RV---FPKVAKCEFVY-GPSGTPNIMDILCVLPLNILNEKIFAVLYVWFL-FALLAIMNILYRLLICCPLRLQLLNPKSHVREVLSAGYGDWFVLMCVSINVNPTLFRELLEQL--D
'Dme-Panxδ07' --L--SV----R-Q-RIDNIVFKLHYRWTVILLVA-TLLITSRQYIGEHIQCL--VVSPVINTFCFFTPTF-VD--P---PGI--D-RHAYYQWVPFVLFFQALCFYIPHALWKW-EGGRIKALVK--LG-MERVKD---IRDM--RLNWG-HVFAEVLNLINLLLQITWTNRFLGGQFLTLG------HALKN-RSDEVV---FPKITKCKFHKFGDSGSIQMHDALCVMALNIMNEKIYIILWFWYAFLLIVTVLGLLWRLCF---VR-WSL----------P-LASNWMFLFFLRSNLS-----E-L----DN
'Dme-Panxδ8'  LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
'Dme-Panxδ12' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
;
end;

Usage example 2

$: alb Drosophila.nex -oi rev

Output

#NEXUS
begin data;
	dimensions ntax=8 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ12' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'Dme-Panxδ8'  LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
'Dme-Panxδ07' --L--SV----R-Q-RIDNIVFKLHYRWTVILLVA-TLLITSRQYIGEHIQCL--VVSPVINTFCFFTPTF-VD--P---PGI--D-RHAYYQWVPFVLFFQALCFYIPHALWKW-EGGRIKALVK--LG-MERVKD---IRDM--RLNWG-HVFAEVLNLINLLLQITWTNRFLGGQFLTLG------HALKN-RSDEVV---FPKITKCKFHKFGDSGSIQMHDALCVMALNIMNEKIYIILWFWYAFLLIVTVLGLLWRLCF---VR-WSL----------P-LASNWMFLFFLRSNLS-----E-L----DN
'Dme-Panxδ6'  MAAVKPLSNYLRLKVRIYDPIFTLHSKCTIVILLTCTFLLSAKQYFGEPILCL-S-SERQADSYCWTMGTYWNEQSIAE--GVETRMYLRYYQWVFMILLFQSLLFYFPSFLWKVWEGQRMEQLCEVDRTRQM--LTRYFPIHWC----YSIYAFCELLNVFISILNFWLMDVVFNGFWYKYIHALW-------NLWM-RV---FPKVAKCEFVY-GPSGTPNIMDILCVLPLNILNEKIFAVLYVWFL-FALLAIMNILYRLLICCPLRLQLLNPKSHVREVLSAGYGDWFVLMCVSINVNPTLFRELLEQL--D
'Dme-Panxδ5'  MSAVKPLSKYLQFKIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-S-EEKNIESYCWTMGTYYNEASIAE--GVEIRQYLRYYQWVIILLLFQSFVFYFPSCLWKVWEGRRLKQLCEVDNTRRM--LVKYFDMHFC----YMAYVFCEVLNFLISVVNIIVLEVFLNGFWSKYLRALW-------DRWV-SV---FPKIAKCELKF-GGSGTANVMDNLCILPLNILNEKIFVFLWAWFL-LALMSGLNLLCRLAICSRLREQMIRTKRHVKRALDLTIGDWFLMMKVSVNVNPMLFRDLMQEL---
'Dme-Panxδ04' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ3'  -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ1'  YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
;
end;