eomegapp |
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Clustal-Omega (clustalo) is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.
In its current form Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become available in a future version.
% eomegapp ../data/op2.ali Profile with profile (ClustalO wrapper) (aligned) protein output sequence set [op1.aln]: |
Go to the input files for this example
Go to the output files for this example
Profile with profile (ClustalO wrapper) Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-aprofile] infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) [-bprofile] infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) [-outseq] seqoutset [ |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||||||||||
[-aprofile] (Parameter 1) |
infile | Pre-aligned multiple sequence file (aligned columns will be kept fixed) | Input file | Required | ||||||||||||||
[-bprofile] (Parameter 2) |
infile | Pre-aligned multiple sequence file (aligned columns will be kept fixed) | Input file | Required | ||||||||||||||
[-outseq] (Parameter 3) |
seqoutset | (Aligned) protein sequence set filename and optional format (output USA) | Writeable sequences | <*>.format | ||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||
(none) | ||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||
-indistfile | infile | Pairwise distance matrix input file (skips distance computation) | Input file | Required | ||||||||||||||
-inguidefile | infile | Guide tree input file (skips distance computation and guide tree clustering step) | Input file | Required | ||||||||||||||
-dealign | toggle | Dealign input sequences | Toggle value Yes/No | No | ||||||||||||||
-cluster | list | Method |
|
mbed | ||||||||||||||
-maxiterations | integer | Number of (combined guide tree/HMM) iterations | Integer from 0 to 2000000000 | 0 | ||||||||||||||
-maxgiterations | integer | Maximum guide tree iterations | Integer from 0 to 2000000000 | 2000000000 | ||||||||||||||
-maxhiterations | integer | Maximum number of HMM iterations | Integer from 0 to 2000000000 | 2000000000 | ||||||||||||||
-maxseqs | integer | Maximum number of sequences | Integer from 2 to 2000000000 | 2000000000 | ||||||||||||||
-maxlenseq | integer | Maximum length of sequence | Integer from 1 to 2000000000 | 2000000000 | ||||||||||||||
-self | toggle | Set options automatically (might overwrite some options | Toggle value Yes/No | No | ||||||||||||||
-outformat | list | Format |
|
fasta | ||||||||||||||
-outdistfile | outfile | Pairwise distance matrix output file, only available in cluster mode 'full' | Output file | <*>.eomegapp | ||||||||||||||
-outguidefile | outfile | Guide tree output file | Output file | <*>.eomegapp | ||||||||||||||
-log | toggle | Log progress to standard output if not used for output | Toggle value Yes/No | No | ||||||||||||||
Associated qualifiers | ||||||||||||||||||
"-outseq" associated seqoutset qualifiers | ||||||||||||||||||
-osformat3 -osformat_outseq |
string | Output seq format | Any string | |||||||||||||||
-osextension3 -osextension_outseq |
string | File name extension | Any string | |||||||||||||||
-osname3 -osname_outseq |
string | Base file name | Any string | |||||||||||||||
-osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |||||||||||||||
-osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |||||||||||||||
-ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||||||||||
-oufo3 -oufo_outseq |
string | UFO features | Any string | |||||||||||||||
-offormat3 -offormat_outseq |
string | Features format | Any string | |||||||||||||||
-ofname3 -ofname_outseq |
string | Features file name | Any string | |||||||||||||||
-ofdirectory3 -ofdirectory_outseq |
string | Output directory | Any string | |||||||||||||||
"-outdistfile" associated outfile qualifiers | ||||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||||
"-outguidefile" associated outfile qualifiers | ||||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||||
General qualifiers | ||||||||||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
>OPSD_ABYKO O42294 Rhodopsin (Fragment) -----------------------------------------YLVNPAAYAALGAYMFLLI LIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVANLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEAFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFTWVMAL ACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAPAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKSAAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_AMBTI Q90245 Rhodopsin MNGTEGPNFYV-------PFSNKSGVVRSPFEYP-----QYYLAEPWQYSVLAAYMFLLI LLGFP---VNFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVFGGFPVTMYSSMHGYFVF GQTGCYIEGFFATMGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVMMTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFLVHFTIPLMIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVAFLICWVPYASVA FYIFSNQGTDFGPIFMTVPAFFAKSSAIYNPVIYIVLNKQFRNCMIT---TICCGKNPFG DDETTSAATSKTEASSVSSSQVSPA >OPSD_ANOCA P41591 Rhodopsin MNGTEGQNFYV-------PMSNKTGVVRNPFEYP-----QYYLADPWQFSALAAYMFLLI LLGFP---INFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVLMGFTTTMYTSMNGYFIF GTVGCNIEGFFATLGGEMGLWSLVVLAVERYVVICKPMSNFRFGETHALIGVSCTWIMAL ACAGPPLLGWSRYIPEGMQCSCGVDYYTPTPEVHNESFVIYMFLVHFVTPLTIIFFCYGR LVCTVKAAAAQQQE-------------SATTQKAEREVTRMVVIMVISFLVCWVPYASVA FYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQFRNCMIM---TLCCGKNPLG DEETSAG--TKTETSTVSTSQVSPA >OPSD_APIME Q17053 Rhodopsin, long-wavelength (Opsin, green-sensitive) MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL GWTIAPMFGWNRYVPEGNMTACGTDYFNRGL--LSASYLVCYGIWVYFVPLFLIIYSYWF IIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVIN FSGIF-NLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSS DAVSTTSGTTTVTD-----NEKSNA >OPSD_ASTFA P41590 Rhodopsin MNGTEGPYFYV-------PMSNATGVVRSPYEYP-----QYYLAPPWAYACLAAYMFFLI LVGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSLNGYFVF GRLGCNLEGFFATFGGINSLWCLVVLSIERWVVVCKPMSNFRFGENHAIMGVAFTWFMAL ACTVPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNESFVIYMFVVHFLTPLFVITFCYGR LVCTVKEAAAQQQE-------------SETTQRAEREVTRMVILMFIAYLVCWLPYASVS WWIFTNQGSEFGPIFMTVPAFFAKSSSIYNPVIYICLNKQFRHCMIT---TLCCGKNPFE EEEGASTTASKTEASSVSSVSPA-- >OPSD_ATHBO Q9YGZ1 Rhodopsin MNGTEGPYFYI-------PMLNTTGVVRSPYEYP-----QYYLVNPAAYAVLGAYMFFLI LVGFP---INFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTIYTSMHGYFVL GRLGCNVEGFSATLGGEIALWSLVVLAIERWVVVCKPISNFRFGENHAIMGVAFTWFMAA ACAVPPLFGWSRYIPEGMQCSCGIDYYTRAEGFNNESFVIYMFTCHFCIPLMVVFFCYGR LVCAVKEAAAAQQE-------------SETTQRAEREVTRMVIIMVVSFLVSWVPYASVA WYIFTHQGSEFGPLFMTIPAFFAKSSSIYNPMIYICMNKQFRHCMIT---TLCCGKNPFE EEEGASSTASKTEASSVSSSSVSPA >OPSD_BATMU O42300 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDNAIMGLAFSWVMAL TCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFPIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVILVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BATNI O42301 Rhodopsin (Fragment) -----------------------------------------YLVSPAAYAALGAYMFLLI LIGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVL GRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRFTEDNAIMGLAFSWVMAL ACAVPPLVGWLRYIPEGMQCTCGVDYYTRAEGFDNESFVIYMFIVHFLIPLSVIFFCYGR LLCAVKEAAAAQQE-------------SETTQRAEKEVSRMVVIMVIGFLVCWLPYASVA WWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI-------------- ------------------------- >OPSD_BOVIN P02699 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEAP-----QYYLAEPWQFSMLAAYMFLLI MLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVF GPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVT---TLCCGKNPLG DDEASTTVS-KTET-----SQVAPA >OPSD_BUFBU P56514 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSILCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFIL GATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMAL SCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG EDDASSAATSKTEASSVSSSQVSPA >OPSD_BUFMA P56515 Rhodopsin MNGTEGPNFYI-------PMSNKTGVVRSPFEYP-----QYYLAEPWQYSVLCAYMFLLI LLGFP---INFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFVF GQTGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAIMGVAFTWIMAL ACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFLIPLIIIFFCYGR LVCTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVVFFLICWVPYASVA FFIFTHQGSEFGPVFMTIPAFFAKSSSIYNPVIYIMLNKQFRNCMIT---TLCCGKNPFG DEDASSAATSKTEASSVSSSQVSPA >OPSD_CALPD Q6W3E1 Rhodopsin MNGTEGPNFYV-------PFSNKTGVVRSPFEEP-----QYYLAEPWQFSCLAAYMFMLI VLGFP---INFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGYFVF GPTGCDLEGFFATLGGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVMAL ACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVVIFFCYGQ LVFTVKEAAAQQQE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVA FYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQFRTCMLT---TLCCGKIPLG DDEASATAS-KTET-----SQVAPA |
>OPSD_CAMHU O18312 Rhodopsin (Fragment) -----------------------------------LHMIHLHWYQYPPMNPMMYPLLLIF MLFTGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMVTCYYHTW TLGPTFCQVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILSVWVL STAWCIAPFFGWNHYVPEGNLTGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKNAMTTVALWFIAWTPCL LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS-------------------- ----------------------------- >OPSD_CAMLU O16017 Rhodopsin (Fragment) -----------------------------------LHMIHLHWYQYPPMNPMMYPLLLVF MLITGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMITCYYHTW TLGATFCEVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILTVWVL SFTWCVAPFFGWNRYVPEGNLTGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS-------------------- ----------------------------- >OPSD_CAMMA O18315 Rhodopsin (Fragment) -----------------------------------LHMIHLHWYQYPPMNPMMYPLLLVF MLITGILCLAGNFVTIWVFMNTKSLRTPANLLVVNLAMSDFLMMFTMFPPMMVTCYYHTW TLGATFCQVYAFLGNLCGCASIWTMVFITFDRYNVIVKGVAGEPLSTKKASLWILTIWIL SITWCIAPFFGWNRYVPEGN-TGCGTDYLSEDI--LSRSYLYIYSTW-VYFLPLAITIYC HVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS-------------------- ----------------------------- >OPSD_CAMSC O16018 Rhodopsin (Fragment) -----------------------------------LHMIHLHWYQYPPMNPMMYPLLLIF MFITGIPCLAGNFVTIWVFMTTKSLRSPANLLVVNLAMSDFLMMFTMFPPMMITCYYHTW TLGPTFCQVYAFLGNLFGCTSIWTMVFITFDRYNVIVKGVAGEPLSNKKAALWILSAWVL SFSWCSAPFFGWNRYVPEGNLTGCGTDYLSEDA--LSRSYLYVYSVW-VYFLPLLITIYC YVFIIKAVAAHEKGMRDQAKKMGIKSLRNEEAQKTSAECRLAKIAMTTVALWFIAWTPYL LINWVGM-FARSYLSPVYTIWGYVFAKANAVYNPIVYAIS-------------------- ----------------------------- >OPSD_CANFA P32308 Rhodopsin -----------------MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAY MFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF VFGPTGCNVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVM ALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEINNESF-VIYMFVVHFAIPMIVIFFC YGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMVIIMVIAFLICWVPYA SVAFYIFTHQGSDFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMIT---TLCCGKN PLGDDEAS---ASASKT---ETSQVAPA- >OPSD_CARAU P32309 Rhodopsin -----------------MNGTEGDMFYVPMSNATGIVRSPYDYPQYYLVAPWAYACLAAY MFFLIITGFPVNFLTLYVTIEHKKLRTPLNYILLNLAISDLFMVFGGFTTTMYTSLHGYF VFGRVGCNPEGFFATLGGEMGLWSLVVLAFERWMVVCKPVSNFRFGENHAIMGVVFTWFM ACTCAVPPLVGWSRYIPEGMQCSCGVDYYTRPQAYNNESF-VIYMFIVHFIIPLIVIFFC YGRLVCTVKEAAAQHE-------------ESETTQRAEREVTRMVVIMVIGFLICWIPYA SVAWYIFTHQGSEFGPVFMTLPAFFAKTAAVYNPCIYICMNKQFRHCMIT---TLCCGKN PFEEEEGASTTASKTEASSVSSSSVSPA- >OPSD_CATBO Q17296 Rhodopsin MMSIASGPSHAAYTWTAQGGGFGNQTVVDKVPPEMLHLVDAHWYQFPPMNPLWHAILGFV [Part of this file has been deleted for brevity] YGRLLCAVKEAAAAQQ-------------ESETTQRSEKEVSRMVVLMVIGFLVCWLPYA STAWWIFCNQGSEFGPVFMTIPAFFAKSSAIYNPMIYICMNKQFRHCMI----------- ----------------------------- >OPSD_CORAU Q90305 Rhodopsin (Fragment) ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----------------------CGIDYYTRAPGYNNESF-VIYMFIVHFLIPLFIISFC YGNLLCAVKAAAAAQE-------------ESETTQRAEREVTRMVIMMVISYLVSWVPYA SVAWYIFSNQGSEFGPVFMTIPAFFAKSSALYNPLIYVLMNKQFRHCM------------ ----------------------------- >OPSD_COTBO O42307 Rhodopsin (Fragment) ----------------------------------------------YLVNPAAYAALGAY MFLLILIGFPINFLTLYVTLEHKKLRTPLNYILLNLAVGNLFMVLGGFTTTMYTSMHGYF VLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRFTEDHAIMGLAFSWVM GLACAVPPLVGWSRYIPEGMKCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLSVIFFC YGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMVVIMVIGFLVCWLPYA SVAWWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFRHCMI----------- ----------------------------- >OPSD_COTGR O42328 Rhodopsin (Fragment) ----------------------------------------------YLVNPAAYAAPGAY MFLLILVGFPVNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYF VLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFSWVM ALTCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLSNNFFC YGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMVVMMVVSFLMCWLPYA SVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKHVRHCMI----------- ----------------------------- >OPSD_COTIN O42330 Rhodopsin (Fragment) ----------------------------------------------YLVNPAAYAALGAY MFLLILIGFPVNFLTLYVTIEHKKLRTPLNYILLNLAVANLFMVLGGFTTTMYTSMHGYF VLGRLGCNLEGFFATMGGEIALWSLVVLAIERWIVVCKPISNFRFTEDHAIMGLAFTWVM ALSCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLTPLIIISFC YGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMVVMMVISFLMCWLPYA SVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKQFRHCMI----------- ----------------------------- >OPSD_COTKE Q90373 Rhodopsin (Fragment) ----------------------------------------------YLVSPAGYAALGAY MFLLILVGFPVNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVLGGFTTTMYTSMHGYF VLGRLGCNLEGFFVTLGGEIALWSLVVLAIERWIGVFKSIRNFRFTEDHAIMGLGFSWVM AATCAVPPLVGWLRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYMFIVHFLIPLIVIFFC YGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMVVIMVIGYLVCWLPYA SVAWWIFCNQGSEFGPIFMTLPAFFAKSPAIYNPLIYICMNKQFPHCMI----------- ----------------------------- >OPSD_CRIGR P28681 Rhodopsin -----------------MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAY MFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF VFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVICKPMSNFRFGENHAIMGVVFTWIM ALACAAPPLVGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYMFVVHFTIPLIVIFFC YGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMVILMVVFFLICWFPYA GVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLT---TLCCGKN ILGDDEAS---ATASKT---ETSQVAPA- |
>OPSD_ABYKO O42294 Rhodopsin (Fragment) ----------------------------------------------------------YL VNPAAYAALGAYMFLLILIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVANLFMVL GGFTTTMYTSMHGYFVLGRLGCNLEAFFATLGGEIALWSLVVLAIERWIVVCKPISNFRF TEDHAIMGLAFTWVMALACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM FIVHFLIPLSVIFFCYGRLLCAVKEAPAAQQE-------------SETTQRAEKEVSRMV VIMVIGFLVCWLPYASVAWWIFCNQGSDFGPIFMTLPSFFAKSAAIYNPMIYICMNKQFR HCMI---------------------------------------- >OPSD_AMBTI Q90245 Rhodopsin -----------------MNGTEGPNFYV-------PFSNKSGVVRSPFEYP-----QYYL AEPWQYSVLAAYMFLLILLGFP---VNFLTLYVTIQHKKLRTPLNYILLNLAFANHFMVF GGFPVTMYSSMHGYFVFGQTGCYIEGFFATMGGEIALWSLVVLAIERYVVVCKPMSNFRF GENHAIMGVMMTWIMALACAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYM FLVHFTIPLMIIFFCYGRLVCTVKEAAAQQQE-------------SATTQKAEKEVTRMV IIMVVAFLICWVPYASVAFYIFSNQGTDFGPIFMTVPAFFAKSSAIYNPVIYIVLNKQFR NCMIT---TICCGKNPFGDDETTSAATSKTEASSVSSSQVSPA- >OPSD_ANOCA P41591 Rhodopsin -----------------MNGTEGQNFYV-------PMSNKTGVVRNPFEYP-----QYYL ADPWQFSALAAYMFLLILLGFP---INFLTLFVTIQHKKLRTPLNYILLNLAVANLFMVL MGFTTTMYTSMNGYFIFGTVGCNIEGFFATLGGEMGLWSLVVLAVERYVVICKPMSNFRF GETHALIGVSCTWIMALACAGPPLLGWSRYIPEGMQCSCGVDYYTPTPEVHNESF-VIYM FLVHFVTPLTIIFFCYGRLVCTVKAAAAQQQE-------------SATTQKAEREVTRMV VIMVISFLVCWVPYASVAFYIFTHQGSDFGPVFMTIPAFFAKSSAIYNPVIYILMNKQFR NCMIM---TLCCGKNPLGDEETSAG--TKTETSTVSTSQVSPA- >OPSD_APIME Q17053 Rhodopsin, long-wavelength (Opsin, green-sensitive) -----------------MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQ YPPLNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMF CMSPPMVINCYYETWVLGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPL SINGALIRIIAIWLFSLGWTIAPMFGWNRYVPEGNMTACGTDYFNRGL--LSASY-LVCY GIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVA LMTISLWFMAWTPYLVINFSGIF-NLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYR AALFAKFPSLACAAEPSSDAVSTTSGTTTVTD-----NEKSNA- >OPSD_ASTFA P41590 Rhodopsin -----------------MNGTEGPYFYV-------PMSNATGVVRSPYEYP-----QYYL APPWAYACLAAYMFFLILVGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVF GGFTTTMYTSLNGYFVFGRLGCNLEGFFATFGGINSLWCLVVLSIERWVVVCKPMSNFRF GENHAIMGVAFTWFMALACTVPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNESF-VIYM FVVHFLTPLFVITFCYGRLVCTVKEAAAQQQE-------------SETTQRAEREVTRMV ILMFIAYLVCWLPYASVSWWIFTNQGSEFGPIFMTVPAFFAKSSSIYNPVIYICLNKQFR HCMIT---TLCCGKNPFEEEEGASTTASKTEASSVSSVSPA--- >OPSD_ATHBO Q9YGZ1 Rhodopsin -----------------MNGTEGPYFYI-------PMLNTTGVVRSPYEYP-----QYYL VNPAAYAVLGAYMFFLILVGFP---INFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVF GGFTTTIYTSMHGYFVLGRLGCNVEGFSATLGGEIALWSLVVLAIERWVVVCKPISNFRF GENHAIMGVAFTWFMAAACAVPPLFGWSRYIPEGMQCSCGIDYYTRAEGFNNESF-VIYM FTCHFCIPLMVVFFCYGRLVCAVKEAAAAQQE-------------SETTQRAEREVTRMV IIMVVSFLVSWVPYASVAWYIFTHQGSEFGPLFMTIPAFFAKSSSIYNPMIYICMNKQFR HCMIT---TLCCGKNPFEEEEGASSTASKTEASSVSSSSVSPA- >OPSD_BATMU O42300 Rhodopsin (Fragment) ----------------------------------------------------------YL [Part of this file has been deleted for brevity] FTVHFLIPLSVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRSEKEVSRMV VLMVIGFLVCWLPYASTAWWIFCNQGSEFGPVFMTIPAFFAKSSAIYNPMIYICMNKQFR HCMI---------------------------------------- >OPSD_CORAU Q90305 Rhodopsin (Fragment) ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------CGIDYYTRAPGYNNESF-VIYM FIVHFLIPLFIISFCYGNLLCAVKAAAAAQE-------------ESETTQRAEREVTRMV IMMVISYLVSWVPYASVAWYIFSNQGSEFGPVFMTIPAFFAKSSALYNPLIYVLMNKQFR HCM----------------------------------------- >OPSD_COTBO O42307 Rhodopsin (Fragment) ----------------------------------------------------------YL VNPAAYAALGAYMFLLILIGFP---INFLTLYVTLEHKKLRTPLNYILLNLAVGNLFMVL GGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISKFRF TEDHAIMGLAFSWVMGLACAVPPLVGWSRYIPEGMKCSCGVDYYTRAEGFNNESF-VIYM FIVHFLIPLSVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMV VIMVIGFLVCWLPYASVAWWIFCNQGSDFGPIFMTLPSFFAKRPAIYNPMIYICMNKQFR HCMI---------------------------------------- >OPSD_COTGR O42328 Rhodopsin (Fragment) ----------------------------------------------------------YL VNPAAYAAPGAYMFLLILVGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVL GGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIALWSLVVLAIERWIVVCKPISNFRF TEDHAIMGLAFSWVMALTCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM FIVHFLIPLSNNFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMV VMMVVSFLMCWLPYASVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKHVR HCMI---------------------------------------- >OPSD_COTIN O42330 Rhodopsin (Fragment) ----------------------------------------------------------YL VNPAAYAALGAYMFLLILIGFP---VNFLTLYVTIEHKKLRTPLNYILLNLAVANLFMVL GGFTTTMYTSMHGYFVLGRLGCNLEGFFATMGGEIALWSLVVLAIERWIVVCKPISNFRF TEDHAIMGLAFTWVMALSCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM FIVHFLTPLIIISFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEREVSRMV VMMVISFLMCWLPYASVAWYIFCNQGSEFGPIFMTLPAFFAKSSAIYNPLIYICMNKQFR HCMI---------------------------------------- >OPSD_COTKE Q90373 Rhodopsin (Fragment) ----------------------------------------------------------YL VSPAGYAALGAYMFLLILVGFP---VNFLTLYVTLEHKKLRTPLNYILLNLAVADLFMVL GGFTTTMYTSMHGYFVLGRLGCNLEGFFVTLGGEIALWSLVVLAIERWIGVFKSIRNFRF TEDHAIMGLGFSWVMAATCAVPPLVGWLRYIPEGMQCSCGVDYYTRAEGFNNESF-VIYM FIVHFLIPLIVIFFCYGRLLCAVKEAAAAQQ-------------ESETTQRAEKEVSRMV VIMVIGYLVCWLPYASVAWWIFCNQGSEFGPIFMTLPAFFAKSPAIYNPLIYICMNKQFP HCMI---------------------------------------- >OPSD_CRIGR P28681 Rhodopsin -----------------MNGTEGPNFYV-------PFSNATGVVRSPFEYP-----QYYL AEPWQFSMLAAYMFLLIVLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVF GGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVICKPMSNFRF GENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYM FVVHFTIPLIVIFFCYGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMV ILMVVFFLICWFPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFR NCMLT---TLCCGKNILGDDEAS---ATASKT---ETSQVAPA- |
[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.
[3] http://www.genetics.wustl.edu/eddy/software/#squid
[4] Wilbur and Lipman, 1983; PMID 6572363
[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
[7] Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
Program name | Description |
---|---|
edialign | Local multiple alignment of sequences |
emma | Multiple sequence alignment (ClustalW wrapper) |
eomega | Multiple sequence alignment (ClustalO wrapper) |
eomegaps | Single sequence with profile (ClustalO wrapper) |
eomegash | Sequence with HMM (ClustalO wrapper) |
eomegasp | Sequence with profile (ClustalO wrapper) |
infoalign | Display basic information about a multiple sequence alignment |
mse | Multiple sequence editor |
plotcon | Plot conservation of a sequence alignment |
prettyplot | Draw a sequence alignment with pretty formatting |
showalign | Display a multiple sequence alignment in pretty format |
tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.