Updated scripts and readme

README.md

@@ -126,7 +126,9 @@ done;
 21a_rscript_ccsel_main.R - execute via Rscript, inputs must be set within the script (pay heed to the comments), must have 21b_rscript_ccsel_auxfunc.R alongside in the same directory to function properly.
 17_rscript_annotscmp_mainjob.R - execute via Rscript, inputs must be set within the script.
 23_rscript_seqstats.R and 24_rscript_ccvissum_mainjob.R - execute via Rscript, see comments in script. These two generate the final tables, plots, and figures.
-25_of_refcomp_prep.R and 26_of_refcomp_mainjob.R - execute via Rscript, see comments in script. These together run an analysis that generates a Venn diagram comparion the actual OrthoFinder run used to detect clock proteins in the paper with an expanded run (with the same parameters) with additional reference proteomes. These additional reference proteomes are basically all the "reference" quality metazoan proteomes in UniProt. These must be downloaded manually, and then 25_of_refcomp_prep.R can be executed on these. Subsequently, 26_of_refcomp_mainjob.bash can be executed to run OrthoFinder, and then 27_rscript_of_refcomp_mainjob.R to generate the Venn diagram.
+25_rscript_of_refcomp_prep.R and 27_rscript_of_refcomp_mainjob.R - execute via Rscript, see comments in script. These together run an analysis that generates a Venn diagram comparion the actual OrthoFinder run used to detect clock proteins in the paper with an expanded run (with the same parameters) with additional reference proteomes. These additional reference proteomes are basically all the "reference" quality metazoan proteomes in UniProt. These must be downloaded manually, and then 25_of_refcomp_prep.R can be executed on these to format the headers and filenames properly for analysis with OrthoFinder. Subsequently, 26_of_refcomp_mainjob.bash can be executed to run OrthoFinder, and then 27_rscript_of_refcomp_mainjob.R can be executed to generate the Venn diagram.
+28a_ncbicomp_mainjob_noslurm.bash and 28b_rscript_ncbicomp_mainjob.R - these together take the rscript_ccsel/cc_cand_sel_pub_table.csv file created by 21a_rscript_ccsel_main.R and the files cc_queries.fasta and species_taxids.csv (place these one level above the outputs/ directory within which rscript_ccsel/cc_cand_sel_pub_table.csv should sit; both are available in this GitHub repository under ncbicomp_files/) to search against NCBI's transcriptome and genome assemblies for the species involved in this study to see if any of the proteins for which no candidates were found using our workflow perhaps have matches in the NCBI data. 28a_ncbicomp_mainjob_noslurm.bash uses entrez esearch and fastq-dump (installed in a conda environment called entrez_conda) to get the assemblies, and uses MMseqs2 (installed in a conda environment called mmseqs2_conda) to search against them with cc_queries.fasta which just contains the 10 bait protein sequences used in this study. Note: the bash script here is NOT a Slurm script.
+29_rscript_ccseqcomp_mainjob.R - used to take all the clock protein categories wherein a species had more than one candidate and investigate whether these sequences are paralogs or the result of sequence variation. Needs the contents of rscript_ccsel/fas_by_type which is genertated by 21a_rscript_ccsel_main.R. This produces some MSA FASTA files and visualizations (these MSAs and visualizations can be found in this GitHub repository under circadian_clock_candidates/multiple_candidate_msa) as well as a histogram of pairwise sequence identity values (this is supplementary file S10).
 ```
 
 - As can be seen from some of the script names above (e.g., `22_rscript_ccsel_main.R`), quite a few scripts use the `R` programming language (`v3.6.0` or greater) and concomitant packages. An exhaustive list of packages used in these scripts (and package versions) can be found in the file `r_packages_used.csv` in the `scripts/` directory. Accessing the scripts through `RStudio` should highlight missing packages automatically and present an option to install them automatically; this does not work for the `Bioconductor` packages nor packages from `GitHub` (e.g., `seqvisr`).

circadian_clock_candidates/multiple_candidate_msa/Acartia_clausii__PDP1e_aln.fasta

@@ -0,0 +1,32 @@
+>Acartia_clausii__PDP1e__TRINITY_DN5258_c0_g1_i1.p1_ORFtype_complete_len_415
+--------MDTPPTGRNILQRVGTPAPTK-------QERR----------SKSSSPSPERNMNMKQENPTFLVPPLWKDS
+LSLENI-ANDFLDSNVTGEVMKLDDFLKELQSSDVQENM------------EDLCGVQSGQGQGMLAQNQDQQMHDVRNQ
+QDPHNRYNL----IRPANIESLRESSDHNPHQQLLQDPHGHQHQQQQQLGHQHHS-----------SRQLQQQQDHHGAG
+GISGPVRPPIMHHVGKPPELYNNHNLQENNNNSGIPQASVRPLVRQNLVSPDDHLQLHDDRLS--------PESKTSLLA
+SKRKERMRTTDDEDSEDDTRSFNGYTSTVCVNFSQDDLRLATIPGQGQDFDPATRRFSEEELKPQPIIRKRKKQFVPEEL
+KNNKYWAKRCKNNEAAKRSREARRLKENQIAMRARFLEEENSALKSEVDNLKKENVDLKQMMVALEEK------------
+LNQ---------LIDKR-------------
+>Acartia_clausii__PDP1e__TRINITY_DN58787_c0_g1_i2.p1_ORFtype_complete_len_324
+----------MVVDVKKLMGRVDCLQQNQWNMDY---DGAMKPLKGKEGNNWNSFPNS---------QTAFLGPQLWEKK
+ISMSN-VDQDFK--NWQGYR-GWN---------ETQQNCQ------------NV-----------GSY-----------Q
+--D-----QQQQHLQAMEQ-----------GFQTLQQGFQTLHQQQIQEWAFNPPKIEPAKMMDT---------------
+----------------SPHSH----HQQSNSSNPSPP-------------------------------------------
+----CRMETK----------ND-----DVEFKVSDDDLALAIVPG--AQFDPKTRCFSAEELKPQPIIRKRAKHFTAEND
+KDDRYWEKRSKNNIAARRSREARRLKENQIALRAAYLEKQNMHLKVTLKRLNIENAHIKVNVDHLLARIVEKQKSMEAER
+INNLNNNLVNNQIINNSNNCSTTNQLQMAN
+>Acartia_clausii__PDP1e__TRINITY_DN4264_c0_g1_i4.p1_ORFtype_complete_len_394
+MQAEAWTGHTQGMTIRDILEKVDLFNVNVQNSQKGTEKHLSKGQDGKTIIE-TND--P---------SSAYLGPKLWDRQ
+ITLDLGLDLDSS--ADEGSISGLS-------CGPRSYGCLSPADGAAGASGIDIGGLSPG-GSGLGSSGMSPVFSKISIE
+VEPKERQRSVSSDLQVMNM-----------EEFLAENGLSLD---------MDPNL--PLE-ICAQT-NIQTNTEIRD--
+-----VKPS----------LQ----MTRPNVIMNVPKVENREVS---VVTAKRGLEADDDVDDPSQVTVVKRASNDFLYA
+ESKRARLEREKAEKK----RKF-----ELELEFDPQDLALATVPG--AQFDPSTRTFDVDELRPQPIIRKRKRIYVPDDN
+KDDRYWNNRVKNNVAARRSREARRLKENQIALRAAYLEKENRVIKMELEDVKFDNTKLATERDILKMK-LAKYEKM----
+------------------------------
+>Acartia_clausii__PDP1e__TRINITY_DN4005_c0_g1_i1.p1_ORFtype_complete_len_327
+MEGTVWNNV----TMNELLDRLQ-------PKQPAMETAA--TLKAKLEAEPNIA--P---------ESAYLGPKLWQKP
+ISLQE---------------------------------------------------------------------------
+--------FNEDDFFVMNI-----------EDFLSENDLDKQHLDRA--MKCDESSPEPDEMRCASPASLSFKSPISPEG
+SSMCSERPSFVLS--PTPATP----SPRPGAATPSP----RPGV---IVSTKKEVNTDNDIHQ-----QLGQERNSFLYA
+ESKRAKMEREKAEKK----RKL-----EAEMEFAPEDLALATVPG--ADFDPRERSFNIEELKPQPIIRKRSKIYVPDSQ
+KDERYWEKRSTNNFAARRSREARRLKENQIALRAAYLERQNNMLKRDLEDTKFENSKLAMERDILKKK-LEKYESMQ---
+------------------------------

circadian_clock_candidates/multiple_candidate_msa/Acartia_clausii__RORa_aln.fasta

@@ -0,0 +1,10 @@
+>Acartia_clausii__RORa__TRINITY_DN50346_c0_g1_i1.p1_ORFtype_internal_len_200
+-------------------------------PVSATNTNTP-------------------QGQLDPA-AGFVDSTTAFPN
+V-GAGSNGRPTPPPSLNIQE---DTIERLQNDPERIRQHLSETVLSAHSLTCLMDNAQIQGAWINQMNPAFLIQFKSKSA
+EDLWMTAAQKLTDVITQIIEFAKMLPGFLKFPQEDQIVLLKAGSFELALLRMSRYYCVEKKAVLFMDQLLPMEAFLSTGN
+TCEMKLVSQIFEFVR
+>Acartia_clausii__RORa__TRINITY_DN52624_c0_g1_i1.p1_ORFtype_internal_len_119
+VITCEGCKGFFRRSQSQACVTNYQCPRQKNCVVDRVNRNRCQFCRLQKCLALGMSRDAVKFGRMSKKQREKVEEEVSFHQ
+ANQRGQNRQPGNSPDSSLVEPPSSTETLFPSNPQFSQQH-----------------------------------------
+--------------------------------------------------------------------------------
+---------------

circadian_clock_candidates/multiple_candidate_msa/Acartia_tonsa__PDP1e_aln.fasta

@@ -0,0 +1,24 @@
+>Acartia_tonsa__PDP1e__TRINITY_DN7306_c0_g1_i1.p1_ORFtype_complete_len_412
+ME--------TPPLGRNILQRVG-----TPAN-----TKQERKSRSESPSPERNMNMKQENPTFLVPPLWKDSLSLENIA
+NDFLDSN-------------------------------------------------VTGEVMKLDDFLKELQSSDVQEDM
+-DDLCGVPGGQGMLQQPQMHDVRNQQDPHNRLYNLIRPANIDSLRESNSDHNQHQQLQGPHGHGQQQLPQHHQSSRQLHQ
+QQQQDLHGGGGSGGPVRPPIMHHVGKPPELYNNHNLQENNNSGIPQASVRPLVRQNMVSPENHM--LQNDRLD----RLD
+RLSPESKKSLA--SKRKERMRTTSEDSEDDSRSFSGYTSTVCVNFSQDDLRLATIPGQVQDFDPATRRFSEEELKPQPII
+RKRKKQFVPEELKNNKYWAKRSKNNEAAKRSREARRLKENQIAMRARFLEEENLSLKNEVENLKKENGDLKQMMVALE--
+-EKLNQLVDKR
+>Acartia_tonsa__PDP1e__TRINITY_DN18110_c0_g1_i4.p1_ORFtype_complete_len_393
+MAEAVWNGHTQGMTIRDILEKVDLFNVSVLNSNQKGTEKQHLSKDTDGK---TIIKVNDPSSAYLGPKLWDKQISLDLGL
+-D-LDSSADEGAAGPSGSGERNSGDASGYGVSSGMSPGFAGISIQGSPKERARSTSSDLQVMNMEEFLAENGLS---LDI
+G-DS--LPINE----------------------VCSGPSVLDY-E------------TSPQGHTNINK------T--L--
+-EF----------RDVKPAIT----RPNVIMNVP----------------KVERQVAAAPKRPITAVLDDTEDDCDGEID
+DPVPNKKPSNEFLYAESKRARLEREKAE-KKRKF-----ELELEFAPEDLALATVPGA--QFDPSTRTFDVEELRPQPII
+RKRKRIYVPDDAKDEKYWNCRIKNNVAARRSREARRLKENQIALRAAYLEKENRVLKQELDDVKFENTKLATERDILKMK
+LAKFEQMM---
+>Acartia_tonsa__PDP1e__TRINITY_DN7042_c1_g1_i1.p1_ORFtype_complete_len_316
+MEETVWNSV----TMKELLDRLEPVKAPVPMNKQSMETAATLKAKLEAE---P---NIAPESAYLGPKLWQKPISLQE--
+-----------------------------------------------------FNEDDFFVMNIEDFLTENDMD---RSK
+LDRA--MKCNEGS--------------PEPEEMRCTSMANLSL-R-------------SPVGSPQQSAM-----S--P--
+-EM----------QAV--PSP----RPGVIVSTK----------------K--------------EVINDV------Q-I
+KPVPE---TNSFLYAESKRARLEREKME-KKRKM-----EEEIEFAAEDLALATVPGV--DFDPKQRSFDVEELKPQPII
+RKRAKIYVPDERKDDRYWEKRCKNNYAARRSREARRLKENQIALRAAYLERQNNMLKRDLEETKFDNTKLAMERDILKKK
+LEKYESML---

circadian_clock_candidates/multiple_candidate_msa/Acartia_tonsa__RORa_aln.fasta

@@ -0,0 +1,8 @@
+>Acartia_tonsa__RORa__TRINITY_DN56378_c0_g1_i1.p1_ORFtype_internal_len_106
+------------------------------------------------------------------------------IR
+QHLSETV--------------------------LSAHTLTCLMDTAQ--IQQAWCNNINPAFLIQFKSKSADDLWMTAAQ
+KLTDVITQIIEFAKMLPGFLKFPQEDQIVLLKAGSFELALLRMSRYYCIEKK
+>Acartia_tonsa__RORa__TRINITY_DN51721_c0_g1_i1.p1_ORFtype_internal_len_160
+CGDKSSGVHYGVITCEGCKGFFRRSQSQACVTNYQCPRQKNCVVDRVNRNRCQFCRLQKCLALGMSRDAVKFGRMSKKQR
+EKVEEEVSFHQAAHHRQQRAPGNSPDSSLVEPPSSTETL--FPSNSQFSQQQTYTEFYGSQFPSQFGATSFDEFV-----
+---DST---TNFA---------------------------------------

circadian_clock_candidates/multiple_candidate_msa/Calanus_helgolandicus__PDP1e_aln.fasta

@@ -0,0 +1,21 @@
+>Calanus_helgolandicus__PDP1e__TRINITY_DN4162_c0_g1_i1.p1_ORFtype_complete_len_406
+----MDGR-------ESTSRTILQKIGSAPVIRRKESESEETNDFDQEVRATNTQKSK--------MNMKQEGPFLVPQL
+WKDSISLENITNDFLES---NVTGEVMNLDDFLKELQV--NELAQQTDELQRHVQTPSHLSQMPHHSP-----PNHRMGH
+MQQEDNRFQP-LIRPANIETLKEPSHPVRPSIMHHVGKPPELHMMQSTSHMDQMGDTHVSLPHREGMQNTLSSKDHTGHG
+IPQASVRPLVRPVIMSSGKHEQ---EHDLSRLEDSKPPASKRMRNMSEGSAYTDDEDDDGSHHNFGGFTSTVCVNFSQDD
+LRLATIPGQEGDFDPATRRFSEEELKPQPIIRKRKKQFVPDELKNNKYWAKRCKNNEAAKRSREARRLKENQIAMRARFL
+EEENTALKGEVEHLKKENSDLKQMMMALEEKLNQMTDSR---
+>Calanus_helgolandicus__PDP1e__TRINITY_DN254_c0_g1_i1.p1_ORFtype_complete_len_338
+----MDGNRNGNGWHGMTIRDILEKVDLSNVSSANEGGSGKLETQKSPV-ITVSSLPKLKPATSVIQTSNPTSAYLGPKL
+WEKSITISNLGLEDEEEEEEEPYCDVMNMEEFLAENNIKMDIME----ER---SPESIQTIEVPVYSPSSFLD-------
+SPQ-PSPQSPPTS-D--------IKPPQRPSIIMA---PK---------------REHTAETKKEIL-------------
+---------------PKGENTFLYAESKRAKLEREK--EERRRK-------------------------LEVELDFAPED
+LALATVPGL--DFDPKERAFDMDELRPQPIIKKRQKLFVPDENKDDRYWDKREKNNVAARRSREARRLKENQIALRAAYL
+EKENKVLKTELDGSNFDNTKLATERDILKRKLSQYESFALHK
+>Calanus_helgolandicus__PDP1e__TRINITY_DN2815_c0_g1_i1.p1_ORFtype_complete_len_327
+MAGVVHQSSHPQGWNGMTIKELLDKVDIDGPKPQE-----------------ISSKAKHEPHHS----PQQHSAYLGPKL
+WDKPISLQQFQED---------DFFVMNIEEFLAENNLQVGNRSNHGSEA---SPEP---EELSCTSPSAVMYPNHGQGH
+SPHTHGPVSPPMASDHRVPIINVPSPAQRPSIIVS---PK---------------DN---SPKRNLL-------------
+---------------PKGGNEFLYTESKRAKLEREK--EERRLR-------------------------NQVDIDFAPED
+IALATVPGA--DFDPRERAFDVDELRPQPIIRKRPKIFVGEDSKDDRYWAKRCKNNVAARRSREARRLKENQIALRAAYL
+ERENTGLKKDLEDANFVNSKLAMERDILKQKLSKYETFPPR-

circadian_clock_candidates/multiple_candidate_msa/Calanus_helgolandicus__PER_aln.fasta

@@ -0,0 +1,24 @@
+>Calanus_helgolandicus__PER__TRINITY_DN15555_c0_g1_i1.p1_ORFtype_complete_len_818
+MLSQDGCTSGSGSRLGSGSREGIEDAYKPPALTEELLVIHNRDMEKNMLTKFKEAKRIGETRFRKDGGKFRAAQESGPKH
+VPRDIIKLKEDKRESGRRNHSSKPEVHLKISVPDNVKKDDQRSLAFNDFHWTSSSGMGTPLDINGISQKADHAGNISFPA
+SHIIQSTLPGGSYQNFIQVPAVYVPIPHPGSIPPEMLPNQVPIGLTMDGSSQNLIPVHISDPVAGFINPMTKTKVSDSES
+DSVRETAIHQSKLPDCLAVNSCMELLQHQDKLQERDTPSSLIKNRHIRIQSRDGSHHTSIKGEPGSALESNASAGASIKE
+QHFTTLALKITDNECSSSQSLYSFVHSSDENNRNDFTAASYSSPNGSPEDSKIISPRLVARPLLSEPFWNENVKLDDHLI
+YKYQLQQHDIEDVLRKDRAKILKMEVPNLVDEQLMEMLADLDFDYQGIDVLFDEDK--DSEEETTSADESSG-ENDDKSH
+RVKMSKDKLYMEKLNIFMEENAPFPNSETNSFNKTTGYFKSDLSNVAYGKTSESSRNLDSFKTFENSQLSGLSYGNPSSS
+FKNPESSDTFENSQSCSGVSQNVCTQTIFEKVFENAVEKSSGSRNQHGDNHSFTSNRPQDKRFRYGRNSDSSSAPEPEKN
+KGEMDQVSTKTKKGKHKSVKTPVEVICSDNTSSDEQTMKSNEVTASRSIKVLPCERSPHEDNHKTQQGKRFRYGSPQASE
+EKDVTQKKKEKKKSESLSKAGFSKTRGQDPRLKQSTDESESSVEYLITSSSVEAGPSSDDQAEKKSEANPDISDMSISNQ
+SSVKEGSDNQSEHGSDSNILE
+>Calanus_helgolandicus__PER__TRINITY_DN28421_c0_g1_i1.p1_ORFtype_3prime_partial_len_143
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------MTNNLI
+FNYQMETQNLGDVLMKDQEALKKMQQPEIVEDQLKELFTELEDGVELEEFLVDFECPPTDEDTETSENEQSGIELEEKIF
+R--NRRKKAHLEKMNIFMEAEAPFPMPDSLRLT---------------------------VHKRENSQLYGSPYYSES--
+--------TFH---SISGG-------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------

circadian_clock_candidates/multiple_candidate_msa/Centropages_hamatus__CRY1_aln.fasta

@@ -0,0 +1,16 @@
+>Centropages_hamatus__CRY1__TRINITY_DN5759_c0_g1_i12.p1_ORFtype_complete_len_533
+---MEPVNILWFRNGLRLHDNISLHHAVKDTTAKFLPLFIFDGETPVTKKCQYNKMQFLLECLEDLDEQLREQGSKLYCI
+KGSPAEVFRKLSKKLKIEKVCFDQDCEPIWLERDNSVKNFCGSHRIEVIESIGGTLWDPLEIIEANGGTPPLTYAQFCHV
+SSGLGSPRRPVDDIDFKTVRFADVSENLMAELGFYTTVPEAHTLGFIKESHHQKVYKGGERRALKYFRRRIVAESDAFVD
+GSFLPNRRDPDILCNPKSLSPDLKFGCLSIKTFYWAIQDAFDGVYQGSPPAKTNFCIVSQLIWREFFYAMSTNNPFYGEI
+KRNPICIRVPWYKDDQALAIFLAGKTGFPFIDAGIRQLKNEGWIHHTVRNALSMFLTRGDLWLSWEHGLDLFLDYLIDAD
+WAVSAGNWMWVSSSAFEKALNSTFDLDPRIYGRRVDAHGEYIKRYIPELKNYPCEYLYDPSSAPLEVQQKAGCIIGQDYP
+AAMVDHDKVSIQNRKNMQDLRDELMRKFNEQ-PPHIKPSDENEVKNFFRLEINGEDP
+>Centropages_hamatus__CRY1__TRINITY_DN11471_c0_g1_i15.p1_ORFtype_complete_len_528
+MEGKEAVNILWFRNGLRLHDNESLHIAASDEKVKVLPLFIWDGETPVTRMSAFNKVEFLVECLQDLDDQLQKVGSNLYCV
+RGQPVAVFEKLHKAFKVKKLCFDQDCEPIWLERDNAVKNFCVKKKIKVCESIGATLWNPLKIIEANDGIPPLTYSIFTHV
+TEAVGPPRRPQPNLDLSKVNFAKLEDNLQVKLNCFNKVPQPEDLGFTKTT-EKKVYKGGETRALKFFNRRIQNEKEAFLD
+GSFLPNIRDPDILNPPKSLSPDLKFGCLSVKTFYWAIMDAFKEVHEGNPPPS--HVIVSQLIWREFFYTMSANNPFYAEI
+FRNPICIDVPWGKDEELLNKYKKGETGYPFIDAGLRQLMQEGWTHHVVRNALSMFLTRGDLWLSWEPGFQLFMEKQIDAD
+WAVCAGNWMWVSSSAFEQALNVSFSLDPRYYGRRFDPHGKYIKKWLPELKNFPEEYIYTPWTASLEVQEEAGCIIGKDYP
+FTIVNHDETVVYNTKMMNKLQQLLMKKYNQQEPEHIKPSGDAEVKNFFRIE------

circadian_clock_candidates/multiple_candidate_msa/Centropages_hamatus__PDP1e_aln.fasta

@@ -0,0 +1,12 @@
+>Centropages_hamatus__PDP1e__TRINITY_DN1673_c0_g1_i8.p1_ORFtype_complete_len_315
+MAVQSLWSGLHMKELLDRIEVPTKMESGPIEKQGKVEVEMMPTAESAFLGPKLWDKSISLQQLNEDDFFVMNIDDFLAEN
+DLQKDKFGKALKENEKSPEPDEMRCTNLNNLNIKPDSP-S-D--TNEENSMDSILPQAWMEVLNAP-SPRPGVIVSTKDC
+KRNMLPKGENTFLYAESKRAKMEREKEEKMRR--------------LEISMDFAPEDLALATVPG--ADFDPKERSFDVE
+ELRPQPIIRKRPKIYVPDMEKDDKYWDKRGKNNVAARRSREARRLKENQIALRAAYLERENNVLKRNLEDSSFENSKLVM
+ELEILKKKLAKYENTA
+>Centropages_hamatus__PDP1e__TRINITY_DN34183_c0_g1_i1.p1_ORFtype_5prime_partial_len_216
+--------------------------------------------------------------------------------
+-------------------------------NLYPHQHPVQDVQIHHQPPKEHGIPQASVRPLVRPVMPSPEKF-----E
+RSNSTDYGPNSE----KRTMSTHSDDEDDMEDGSVEGDEDGFQGGFSSSLVNFSEDDLRLATIPGQGQEFDPSTRRFAEE
+ELKPQPIIRKRKKQFVPDELKNNKYWAKRCKNNEAAKRSREARRLKENQIAMRARYLEEENNALKGEMEGLKKENTDLKQ
+MMVALEEKLNQLAESR

circadian_clock_candidates/multiple_candidate_msa/Centropages_hamatus__TIM_aln.fasta

@@ -0,0 +1,38 @@
+>Centropages_hamatus__TIM__TRINITY_DN22370_c1_g1_i6.p1_ORFtype_complete_len_1277
+MNNHVMFGVSDGSTHLGQKVCNKYVIQSGTAATLEIMNRQLNEDDKTLRTYRRALAFSNVIEKDLIPIMLNCNDEPLVFS
+SLLKLFVNLTLPIECIFPAGE-NLSTSSKQTVILLNNVLSKCKVLCSNGQFSWVLMGHLSALCQGA--KESKESISIIHN
+CLLLIRNVLHIPETVSSMKSGC-GQNQIIWNLFSNNLDKVMLELIGHKSASVWCSTIVHIIAILFKDQYGENMAKLLNS-
+--SLAESSTDGESNTSPNDGSPYRNPESDGNSDDIQPTPGQSDAGYPENFQPYPRSRSESVSSLEVFPNASPAQSIISND
+DLDSDEKFGKD------------------------QEWGPA-GLPEGANKGPHSKEEGKARDLEKKETERAATTQIRWGD
+KPEWSSSGIESIGAW-DQ-----GRSSEGRSEVCAEEE-ARKKPC----------------------WSAYREAR-GAED
+KET---KQRENGFG--VNS-----GESSEGEPPEKKSIHENTDRTLHVQFKRNPRPEMQLCHKDKRGPAGPKV------S
+DMESVSDSSETMGVPKKTLEDGSKFAVGFVSHISTIDNERQAALEDSTSSNDDDMLKERYFKSRAHLIKPKPRPGVTLSL
+KAKSELRRMKLLKQVQENRIRCLSMQSI-IGDKEIAELLKEFTVAFLITGYPKLVGDLK--DMLSEKHSNSLDHSNLLWL
+LSYFLQFASQIELGLDQIGSVLSVQTIAFLTFEGVDVVEVLELAA-REPGTDISPHLRRIHLVVTAIREFLQTVNSYSAF
+KHLDSSEKAQLEQVQVQIASMKGLRQLLLLLMRTYNPEIQSVQYLADVVVCNHLVVSSMKADNNSSELTLKTHLTQFANT
+ELMRQYGRLLVDYRTNSEVVNDCIFTMMHHVAGDLEAPHTLHIPSVLNTFSTIWEEGLDICEDWFDLIEYIIQMFLQAMR
+NTPHSCAANIVDNMDSTQVLDGCGMTGNQASQLFWVFSQVENMEDPVGSLIEVYRQTDHIVLSRLAVIQSLLSHGVITHA
+MYMNFIYMNSVMPHTHIDQVESLIAEVGSVHNTDGMNTDEETDAREINTESNQLDNHQVNHQLDNSLPEINLNTTPGNNS
+QKTNLNAEIKTKMNANNNPREISSQEMSSKGNPQEIEEINVLKECLIKQGQYCLISWVQEVLLDACRVKLNPETLIPEPD
+SFTNESVPFYYNHAKQSIPLVPYNRSQYQGLQTESFIFLLHKLGFLLPADVGKAYPRIPYFWSAEQMHEVASKLGPLREG
+EMILNSSMKRKLPSVSSEQELNIKMKKESPDVNSTEESSKNEPTQFMDTGLDGMDLTGET-DRQVGVVR----ASWLQFA
+KLSV
+>Centropages_hamatus__TIM__TRINITY_DN9829_c0_g1_i8.p1_ORFtype_complete_len_1123
+MGDHVVFGVGESVAQLGHQIGSRYMIHDQTSAILETMNRRLNEDDTNLWTYRRALAFSNVIEKDLIPILMNSNEDKVVFN
+AVVKLLVNLSLQAESILPVHVMNNYPAGKQTIHEINSALAKTKALFTNSQFSLVLMKNLSELSQKIDSKQHEHDIVSISN
+CLVLIRNILHIPSKEGTSKSGAGGQNQMIWNLFVQNIDKVILQLISHRSSSVWCTTIVQIIAVLYKDQHVVELERLVKVF
+LDNSLESSGDDESNTGGAD-------------------------------QSWPSSR-NSISSLEVFP-ASPSPTIRSRG
+DEDETQQWYPDEEIITDDDAEAREISVECPGIGTLVEGGPCEGRPGGEGRNEKSGKVG---------A-------ERSGK
+GRSWSNSMDERSGKGRSRGNSMDERSDKGKSGSNSLDERSDKGKSGSNSLDERSDKGKSGSNSMDESFKTMTEAKRIITD
+LVTYSGQGRSYVFKDMVSSSSSSDEQETTEEPPEKKLILEDRNKQKKIKFRRKVRTATDLSRKVCKGPSSSIEQQCDNKS
+GWGSSQDSNENTGVPKKTNGIDCSTKPGFGP-GKQYDTDHQADIEDSVSSSETNN--YLHWAPRSHPVKPKPRPPALFTP
+EERMLHRRQKILKLSHENMVRVKALQNHSAKDKDISELLREFTVTFLIAGYSKLVQDLLTKFMAKEQGRISMDKSHFLWL
+VTYFLKFACPLEIGLEEIGSVLSVETIGYIIYEGVEIVETLKLASTRLPRSDTSPELRRMHLVVTAIREYLQVLYNYINI
+NN-KTSNKQHLEQLKEQAGQMKALRQMLLLFIRSYNQETQSYQYLADLVVCNSLVLNNMES----STTELRNHMTQFANK
+ELMEQYGHLLLDHTQNSVQVNDCVLTMLHHVSGDLEAPHTLYIPSILKTFVALSEEGGALYEDWVDLIHFTIQTFLQRMV
+GG-----------------------------------------------EVEADPPTE----------------------
+---------------HQTQV-------G---RTAGVEL-------------DTLNN------------------------
+------------------------------------NEVHTLTNQIIKEGQGSLITWLQEFFIQVARVKLHPDRLAPAEG
+QIL-DPVVFFYNYSQQSIPLIPFSTLQSKGCQTELFNRLLLELGFILPVDSGKVYPRIPHCWSAQHLYSVATQLGPLTDS
+QLTVADLTA----------------LKEKTWYSSTSMQPLEESMDMMDVGLTSLELPNDRGQKQVARLQAGSGSAWMLLA
+NLSK

circadian_clock_candidates/multiple_candidate_msa/Corystes_sp__CYC_aln.fasta

@@ -0,0 +1,20 @@
+>Corystes_sp__CYC__TRINITY_DN36011_c0_g1_i1.p1_ORFtype_internal_len_155
+PCSPIVLNYLIPMSFPNCPNLFFLSLSFPLFSYHSKLIYRSLIAFPPEQEVKGSSGRMFGLGNFDYPSKYRSECSSIASY
+SSDNGSKKRRGSFLDSNDEDADSIKIPRTSGEWSKRQNHSEIEKRRRDKMNTYIMELSSIIPVCTSRKLDKLTVL-----
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------
+>Corystes_sp__CYC__TRINITY_DN7745_c1_g2_i1.p1_ORFtype_3prime_partial_len_615
+---------------------------------------------------------MFGLGNFDYP-KFRSECSSIASY
+SSDNGSKKRRGSFLDSNDDEGDSIKIPRTSGEWNKRQNHSEIEKRRRDKMNTYIMELSSIIPVCTSRKLDKLTVLRMAVQ
+HMKMLRGSLNSYTEGHYKPAFLSDDELKNLILQPLQAADGFLFVVGCDRGRILYVSESVYQTLHHTQGELLGTSWFDILH
+PKDLTKVKEQLSCSDISRRERLVDAKTLLPVKTDVPQGLTKLCPGSRRAFFCRMRCKSAPVLKEEADSSTGCPKKKSKSQ
+SSDKKYSVIHFTGYLKSWAPTKDPLEEDSGSDSESCNLSCLVAVGRVHQPLLSSGAQDAARFGRTVPPQSIDFISKHTSD
+GKFVFIDQRASLLLGWLPQELLGSSMYEYFHQDDIPFLADTHRSTLQSSESCNTQVYRFRTKDGSFVRLQSVWWTFKNPW
+TKDIEYIISKNSVVTSEAGLVESTMANDSVSQSFNSFNEFLSSPGNCIPDTPPPSNSASSNTNNRLIGGGMHAGKIGRQI
+ADEVLDSQRRNDSASNSPVSPFEGILGTGASDRSFATLLRSDMTAHRSNVKNNVLLSSNTSSCSGSDTSRGPQLNSTTTT
+TPNNNHHHNNHNHNHHHNNHHHHTNNSNIPASD