# HG changeset patch
# User rnateam
# Date 1434466456 14400
# Node ID 8817d3a35fac3f4b1329c2bd590901868a5d0fe4

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 4e6896fc58abc9a6f90d97aaf80fde006a071a7d-dirty

diff -r 000000000000 -r 8817d3a35fac mafft.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft.xml	Tue Jun 16 10:54:16 2015 -0400
@@ -0,0 +1,157 @@
+<tool id="rbc_mafft" name="MAFFT" version="7.221.0">
+    <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+    <requirements>
+        <requirement type="package" version="7.221">mafft</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <version_command>
+    <![CDATA[
+        mafft --version
+    ]]>
+    </version_command>
+    <command>
+    <![CDATA[
+        #if $cond_flavour.flavourType != 'custom'
+            $cond_flavour.flavourType
+        #else
+            ### full parameter options
+            mafft
+        #end if
+        
+        #if $cond_outformat.outputFormat == 'clustalw'
+            --clustalout
+        #end if
+        
+        $inputSequences > 
+        
+        #if $cond_outformat.outputFormat == 'fasta'
+            $outputFasta
+        #else ## $cond_outformat.outputFormat == 'clustalw'
+            $outputClustalW
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+        <conditional name="cond_flavour">
+            <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
+                <option value="mafft-fftns" selected="true">fftns</option>
+                <option value="mafft-fftnsi">fftnsi</option>
+                <option value="mafft-nwns">nwns</option>
+                <option value="mafft-nwnsi">nwnsi</option>
+                <option value="mafft-einsi">einsi</option>
+                <option value="mafft-ginsi">ginsi</option>
+                <option value="mafft-linsi">linsi</option>
+                <option value="mafft-qinsi">qinsi</option>
+                <option value="mafft-xinsi">xinsi</option>
+                <option value="custom">Custom Parameters</option>
+            </param>
+            <when value="mafft-fftns"/>
+            <when value="mafft-fftnsi"/>
+            <when value="mafft-nwns"/>
+            <when value="mafft-nwnsi"/>
+            <when value="mafft-einsi"/>
+            <when value="mafft-ginsi"/>
+            <when value="mafft-linsi"/>
+            <when value="mafft-qinsi"/>
+            <when value="mafft-xinsi"/>
+            <when value="custom"/>
+        </conditional>
+        <conditional name="cond_outformat">
+            <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
+                <option value="fasta" selected="true">FASTA</option>
+                <option value="clustalw">ClustalW</option>
+            </param>
+            <when value="fasta"/>
+            <when value="clustalw"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
+            <filter>(cond_outformat['outputFormat'] == 'fasta')</filter>
+        </data>
+        <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
+            <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputSequences" value="sample"/>
+            <param name="flavourType" value="fftns"/>
+            <param name="outputFormat" value="fasta"/>
+            <output name="outputFasta" file="sample.fftns2"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+**What it does**
+
+MAFFT is a multiple sequence alignment program for unix-like operating systems.  
+It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 
+FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
+
+From the MAFFT man page, an overview of the different predefined flavours of the tool.
+
+**Accuracy-oriented methods:**
+
+- L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
+    
+    - mafft --localpair --maxiterate 1000 input [> output]
+
+- G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
+    
+    - mafft --globalpair --maxiterate 1000 input [> output]
+
+- E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
+    
+    - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. 
+
+
+**Speed-oriented methods:**
+
+- FFT-NS-i (iterative refinement method; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 input [> output]
+
+- FFT-NS-i (iterative refinement method; max. 1000 iterations):
+
+    - mafft --retree 2 --maxiterate 1000 input [> output]
+
+- FFT-NS-2 (fast; progressive method):
+
+    - mafft --retree 2 --maxiterate 0 input [> output]
+
+- FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
+
+    - mafft --retree 1 --maxiterate 0 input [> output]
+
+- NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 --nofft input [> output]
+
+- NW-NS-2 (fast; progressive method without the FFT approximation):
+
+    - mafft --retree 2 --maxiterate 0 --nofft input [> output]
+
+- NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
+
+    - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
+    
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/molbev/mst010</citation>
+        <citation type="doi">10.1093/nar/gkt389</citation>
+        <citation type="doi">10.1093/bioinformatics/bts578</citation>
+        <citation type="doi">10.1093/bioinformatics/btq224</citation>
+        <citation type="doi">10.1007/978-1-59745-251-9_3</citation>
+        <citation type="doi">10.1186/1471-2105-9-212</citation>
+        <citation type="doi">10.1093/bib/bbn013</citation>
+        <citation type="doi">10.1093/bioinformatics/btl592</citation>
+        <citation type="doi">10.1093/nar/gki198</citation>
+        <citation type="doi">10.1093/nar/gkf436</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 8817d3a35fac test-data/sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample	Tue Jun 16 10:54:16 2015 -0400
@@ -0,0 +1,285 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+>     8=opsin, greensensitive  human (fragment) S07060
+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
+PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
+IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
+GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
+GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
+VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
+LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
+SVAPA
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
+VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
+PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
+TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
+LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
+AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
+PA
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
+KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
+SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
+CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
+EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
+MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
+LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
+QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
+MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
+YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
+GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
+KAPESSAVASTSTTQEPQQTTAA
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
+GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
+YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
+SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
+APESRAAISTSTTQEQQQTTAA
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
+PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
+VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
+LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
+ISSAQSTTTQEQQQTTAA
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
+FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
+ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
+TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
+IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
+SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
+EASSAQSTTTQEQTQQTSAA
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
+WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
+IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
+SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
+KSNDDSQSNSTVAQDKA
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
+WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
+ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
+TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
+NDVEENQSSNTQTQEKS
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
+GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
+RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
+AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
+CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
+VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
+FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
+QSQATASEAESKA
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
+CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
+AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
+LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
+AQSQATTSEAESKA
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
+WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
+YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
+EPKPDAPASDTETTSEADSKA
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
+WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
+YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
+EPKPDAPPSDTETTSEAESKD
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
+MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
+GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
+GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
+QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
+GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
+STTSGTTTVTDNEKSNA
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
+CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
+EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
+PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
+HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
+SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
+ASATTTMEEKPKIPEA
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
+SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
+FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
+EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
+RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
+PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
+GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
+QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
+KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
+MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
+GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
+LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
+VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
+DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
+PPPPQGAPPQGAPPAAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
+DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
+LAERPERPEFVLQNADYCRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RQ
+>    33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RR
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
+VFSPEFRHAFQRLLCGRRVRRRRAPQ
diff -r 000000000000 -r 8817d3a35fac test-data/sample.fftns2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.fftns2	Tue Jun 16 10:54:16 2015 -0400
@@ -0,0 +1,504 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+-------------------MNGTE------------------------GDNF--------
+YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----
+----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F
+TVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FR
+FGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNN
+ESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------
+---------------------------------------------------AAAAQQ---
+------------------------------------------------------------
+--------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-
+HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN
+PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------
+--------------------------------------------SPA-------------
+------
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+-------------------MNGTE------------------------GPNF--------
+YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----
+----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F
+TTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FR
+FGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNN
+ESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-
+HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN
+PLGD-DE--ASATASKTE------TSQV--------------------------------
+--------------------------------------------APA-------------
+------
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+-------------------MNGTE------------------------GINF--------
+YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----
+----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F
+TVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FR
+FSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHN
+ESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-
+NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC---------GKN
+PFGD-EDVSSTVSQSKTEVSSVS-SSQV--------------------------------
+--------------------------------------------SPA-------------
+------
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+-------------------MNGTE------------------------GKNF--------
+YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F
+TVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+FSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNN
+ESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-
+NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC---------GKN
+PLGD-DE-SSTVSTSKTEVSS------V--------------------------------
+--------------------------------------------SPA-------------
+------
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+-------------------MNGTE------------------------GNNF--------
+YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----
+----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F
+TVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK
+FSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNN
+ESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA------------------------
+---------------------------------------------------AAAQQQ---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-
+NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC---------GKN
+PLGD-EE-SSTVSTSKTEVSS------V--------------------------------
+--------------------------------------------SPA-------------
+------
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+-------------------MKQVPEF----------------------HEDF--------
+YIPIPLDI-NNLS--AYSPF----------------LVPQD-------HLGNQGI-----
+----FMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-S
+PLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FT
+FKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNN
+ESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KL------------------------
+---------------------------------------------------AAKAQA---
+------------------------------------------------------------
+--------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-
+HRGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC---------GKN
+-IEE-DE--ASTSSQVTQVSS------V--------------------------------
+--------------------------------------------APEK------------
+------
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+-------------------MRKMS------------------------EEEF--------
+YL-----F-KNIS--SVGPW----------------DGPQY-------HIAPVWA-----
+----FYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-V
+FPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FR
+FSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRS
+ESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KA------------------------
+---------------------------------------------------VAAQQQ---
+------------------------------------------------------------
+--------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-
+NRNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC---------GKA
+-MTD-ES--DTCSSQKTEVSTVS-STQV--------------------------------
+--------------------------------------------GPN-------------
+------
+>     8=opsin, greensensitive  human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------------------DLAETVIA-S
+TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMVLAFC----------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+-------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+----YHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VR
+FDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-
+NPGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    10== Z68193   1 human Red Opsin <>[]
+-------------------MAQQWSL----------QRLAGRHPQDSYEDST--------
+QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----
+----YHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-S
+TISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VR
+FDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGV
+QSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RA------------------------
+---------------------------------------------------VAKQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-
+NPGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--ELSSASKTEVSSV---SSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+-------------------MTEAWNV----------AVFAARRSRDD-DDTT--------
+RGSV-FTY-TNTNN-TRGPF----------------EGPNY-------HIAPRWV-----
+----YNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-S
+TISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IK
+FDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGC
+QSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RA------------------------
+---------------------------------------------------VAAQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-
+NPGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF----------GKK
+-VDD-GS--EASTTSRTEVSSVS-NSSV--------------------------------
+--------------------------------------------APA-------------
+------
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+-------------------MA-AWEA----------AFAARRRHEE--EDTT--------
+RDSV-FTY-TNSNN-TRGPF----------------EGPNY-------HIAPRWV-----
+----YNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-S
+TISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IK
+FDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGV
+QSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RA------------------------
+---------------------------------------------------VAAQQK---
+------------------------------------------------------------
+--------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-
+NPGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF----------GKK
+-VDD-GS--EVST-SRTEVSSVS-NSSV--------------------------------
+--------------------------------------------SPA-------------
+------
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+-------------------MS---------------------------SNSS--------
+QAP--------PNG-TPGPF----------------DGPQW------PYQAPQST-----
+----YVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-S
+SVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQ
+FQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--
+NSYILSLFVTCFVLPLSLILFSYTNLLLTL----RA------------------------
+---------------------------------------------------AAAQQK---
+------------------------------------------------------------
+--------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-
+HKGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY-----QPQR
+-TGK-AS--PGTPGPHADVTAAGLRNKV--------------------------------
+--------------------------------------------MPAHP---V-------
+------
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+----------MESGNVSSSLFGNVST----------ALRPEARL----SA----------
+-ETRLLGW--------NVPP----------------EELR--------HIPEHWLTYPEP
+PESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--T
+PIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--K
+MTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDT
+RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LRDQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-
+GDKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL--------N
+EKAP-ES-SAVASTSTTQEP-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+----------MEYHNVSSVL-GNVSS----------VLRPDARL----SA----------
+-ESRLLGW--------NVPP----------------DELR--------HIPEHWLIYPEP
+PESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--T
+PIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--K
+MTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDT
+RLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LRDQAKKM-
+--------------------------------NVDSL-----------------------
+-----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-
+GDKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI--------S
+EKAP-ES-RAAISTSTTQEQ-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+----------ME------PLCNASEP----------PLRPEAR-----SSGN--------
+GDLQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+PASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+RLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+GDKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV--------N
+EKSG-EI-SSAQST-TTQEQ-QQ-TTAA--------------------------------
+------------------------------------------------------------
+------
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+----------MD------ALCNASEP----------PLRPEARM----SSGS--------
+DELQFLGW--------NVPP----------------DQIQ--------YIPEHWLTQLEP
+PASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--A
+PIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--N
+MTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDT
+RLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVESL-----------------------
+-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-
+GDKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV--------N
+EKSG-EA-SSAQST-TTQEQTQQ-TSAA--------------------------------
+------------------------------------------------------------
+------
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+-------------------MTNATGP----------QMAYYGAA----SMD---------
+-----FGYPEGVSIVDFVRP----------------EIKP--------YVHQHWYNYPPV
+NPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-V
+PFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PK
+LTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNT
+FSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA------------------------
+---------------------------------------------------MRAQAKKM-
+--------------------------------NVSTL-----------------------
+-----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-
+GDTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HET
+ETKS-ND-DSQSNSTVAQDKA---------------------------------------
+------------------------------------------------------------
+------
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+-------------------MANVTGP----------QMAFYGSG----AAT---------
+-----FGYPEGMTVADFVPD----------------RVKH--------MVLDHWYNYPPV
+NPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-F
+PPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PK
+LTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNT
+ITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA------------------------
+---------------------------------------------------MRAQAKKM-
+--------------------------------NVTNL-----------------------
+-----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-
+GNAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HEK
+DPND-VE-ENQSSNTQTQEKS---------------------------------------
+------------------------------------------------------------
+------
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+----------ME---SFAVAAAQLGP----------HFAPLS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKM---------------------------YVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-DAQSQATASEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+----------ME---SFAVAAAQLGP----------HFAPLS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWNQFPAM
+DPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-DAQSQATASEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+----------MD---SFAAVATQLGP----------QFAAPS------------------
+----------NGSVVDKVTP----------------DMAH--------LISPYWDQFPAM
+DPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-T
+PMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RP
+MTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNP
+RSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-
+KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GKV
+DDGK-SS-EAQSQATTSEAESKA-------------------------------------
+------------------------------------------------------------
+------
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+-----MERSHLP---ETPFDLAHSGP----------RFQAQSSG----------------
+----------NGSVLDNVLP----------------DMAH--------LVNPYWSRFAPM
+DPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+MTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNP
+RSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-
+KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GNT
+DEPKPDA-PASDTETTSEADSKA-------------------------------------
+------------------------------------------------------------
+------
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+-----MERSLLP---EPPLAMALLGP----------RFEAQTGG----------------
+----------NRSVLDNVLP----------------DMAP--------LVNPHWSRFAPM
+DPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-S
+PVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TP
+MTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNP
+RSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKA------------------------
+---------------------------------------------------MRDQAKKM-
+--------------------------------NVKSL-----------------------
+-----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-
+KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GTT
+DEPKPDA-PPSDTETTSEAESKD-------------------------------------
+------------------------------------------------------------
+------
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+-------------------MIAVSGP----------SYEAFSYG----GQA---------
+----RF---NNQTVVDKVPP----------------DMLH--------LIDANWYQYPPL
+NPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-S
+PPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KP
+LSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLS
+ASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN------------------------
+---------------------------------------------------MREQAKKM-
+--------------------------------NVASL-----------------------
+-----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-
+NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------AA
+EPSS-DA-VSTTSGTTTVTDNEK-SNA---------------------------------
+------------------------------------------------------------
+------
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+---------------------MANQL----------SYSSLGWP----YQP---------
+----------NASVVDTMPK----------------EMLY--------MIHEHWYAFPPM
+NPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-M
+PTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-AP
+LTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSS
+ASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ------------------------
+---------------------------------------------------LREQAKKM-
+--------------------------------NVASL-----------------------
+-----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-
+SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GSG
+ESGS-DV-KSEASATTTMEEKPK-IPEA--------------------------------
+------------------------------------------------------------
+------
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+------------------------------------MVESTTLV----NQT---------
+-----WWY--NPTVD----------------------------------IHPHWAKFDPI
+PDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGF
+PLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKK
+MSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPST
+RSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE------------------------
+---------------------------------------------------MAAMAKRL-
+--------------------------------NAKEL-----------------------
+-----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-
+GPAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKEC
+EDAN-DA-EEEVVASER--GGES-RDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
+QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA
+------
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+-------------------------------------MGRDLRD----NET---------
+-----WWY--NPSIV----------------------------------VHPHWREFDQV
+PDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGF
+PLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKK
+MSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTT
+RSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKE------------------------
+---------------------------------------------------MAAMAKRL-
+--------------------------------NAKEL-----------------------
+-----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-
+GPLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKET
+EDDK-DA-ETEIPAGESSDAAPS-ADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
+QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA
+------
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+---------MMD-------VNSSGRPDLYGHLRSF-LLPEVGRGLPDLSPDGGADPVAGS
+WAPHLLS---EVTASPAPTW----------------DAPPDNASGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VEPDS----
+---VIAL-----------------NGIVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERPEFVLQNADYCR
+KKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+------------------------------------------------------------
+-MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VQPES----
+---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERSEFVLQNSDHCG
+KKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+------------------------------------------------------------
+-MPHLLSGFLEVTASPAPTW----------------DAPPDNVSGCGEQIN--------Y
+GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-M
+PFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVR
+QNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF---------
+-GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF---------------------
+----------------------------------P--------GFPR----VQPES----
+---VISL-----------------NGVVKLQ--------KEVEECAN-------------
+-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFI
+CGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------
+-----NINRKLSAAGMHEALKLA-------------------------------------
+-------------------------------------------ERPERSEFVLQNSDHCG
+KKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+----------MD-------VLSPG------------QGNNTTSPPAPFETGG--------
+----------NTTGISDVTV----------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-
+--------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG-
+-PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+-----RQ-----------------------------------------------------
+------------------------------------------------------------
+------
+>    33=p A35181 serotonin receptor class 1A - rat
+----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------
+----------NVTSISDVTF----------------------------------------
+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L
+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK
+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------
+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------
+---------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-
+--------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG-
+-SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-
+CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------
+-----RR-----------------------------------------------------
+------------------------------------------------------------
+------
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+-GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+-----RGHR---------------------------------------------------
+------------------------------------------------------------
+------
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------
+----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY
+SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M
+PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR
+RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------
+-GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE
+YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--
+--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-
+------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-
+VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------
+-----RGHR---------------------------------------------------
+------------------------------------------------------------
+------
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+-MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------
+----------NVTVVPNTTW---------WQASAPFDTPAALVRAAAK------------
+--------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M
+PLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHA
+STAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV---------
+-GYQIFATASSFYVPVLIILILYWRIYQTARKRIR-------------------------
+--------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGI
+AAAVVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGA
+VAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-
+CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------
+-----RRRRA--------------------------------------------------
+---------------------------------------------PQ-------------
+------
diff -r 000000000000 -r 8817d3a35fac tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 16 10:54:16 2015 -0400
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="mafft" version="7.221">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/MAFFT/mafft-7.221-with-extensions-src.tgz</action>
+                <action type="change_directory">./core</action>
+                <action type="shell_command">sed -i "s|\(PREFIX = \).*$|\1$INSTALL_DIR|" Makefile</action>
+                <action type="shell_command">make clean; make; make install</action>
+                <action type="change_directory">../extensions</action>
+                <action type="shell_command">sed -i "s|\(PREFIX = \).*$|\1$INSTALL_DIR|" Makefile</action>
+                <action type="shell_command">make clean; make; make install</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>