Bio-MUST-Core
14 results

 view release on metacpan or  search on metacpan

bin/classify-ali.pl  view on Meta::CPAN 

with organisms instead of sequences, whereas 'min_copy_mean' and
'max_copy_mean' allow bounding the mean number of gene copies per organism.
All default not no bound.

An example YAML file follows:

    categories:
    - label: strict
      description: strict species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
        min_seq_count: 1
        max_seq_count:
        min_org_count:
        max_org_count:
        min_copy_mean:
        max_copy_mean:
      - tax_filter: [ +Protopterus ]
      # min_seq_count defaults to 1
      # max_seq_count defaults to no upper bound
      # all other also default to no bound
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Xenopus ]
      - tax_filter: [ +Anolis, +Gallus, +Meleagris, +Taeniopygia ]
      - tax_filter: [ +Mammalia ]
    - label: loose
      description: loose species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
      - tax_filter: [ +Protopterus ]
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Amphibia, +Amniota ]

=for Euclid: file.type: readable

=item --taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

bin/tax-mask-ali.pl  view on Meta::CPAN 

with organisms instead of sequences, whereas 'min_copy_mean' and
'max_copy_mean' allow bounding the mean number of gene copies per organism.
All default not no bound.

An example YAML file follows:

    categories:
    - label: strict
      description: strict species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
        min_seq_count: 1
        max_seq_count:
        min_org_count:
        max_org_count:
        min_copy_mean:
        max_copy_mean:
      - tax_filter: [ +Protopterus ]
      # min_seq_count defaults to 1
      # max_seq_count defaults to no upper bound
      # all other also default to no bound
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Xenopus ]
      - tax_filter: [ +Anolis, +Gallus, +Meleagris, +Taeniopygia ]
      - tax_filter: [ +Mammalia ]
    - label: loose
      description: loose species sampling
      criteria:
      - tax_filter: [ +Latimeria ]
      - tax_filter: [ +Protopterus ]
      - tax_filter: [ +Danio, +Oreochromis ]
      - tax_filter: [ +Amphibia, +Amniota ]

=for Euclid: file.type: readable

=item --taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

lib/Bio/MUST/Core/Taxonomy.pm  view on Meta::CPAN 


# example of input HashRef for tax_classifier
# 'min', 'max' and 'description' keys are both optional
# categories => [
#                 {
#                   criteria => [
#                                 {
#                                   max => undef,
#                                   min => 1,
#                                   tax_filter => [
#                                                   '+Latimeria'
#                                                 ]
#                                 },
#                                 {
#                                   tax_filter => [
#                                                   '+Protopterus'
#                                                 ]
#                                 },
#                                 {
#                                   tax_filter => [
#                                                   '+Danio',

lib/Bio/MUST/Core/Taxonomy.pm  view on Meta::CPAN 

#                                                 ]
#                                 }
#                               ],
#                   description => 'strict species sampling',
#                   label => 'strict'
#                 },
#                 {
#                   criteria => [
#                                 {
#                                   tax_filter => [
#                                                   '+Latimeria'
#                                                 ]
#                                 },
#                                 {
#                                   tax_filter => [
#                                                   '+Protopterus'
#                                                 ]
#                                 },
#                                 {
#                                   tax_filter => [
#                                                   '+Danio',

test/G12210-O-S-1-NO.data  view on Meta::CPAN 

0.027730	0.133860	'Pseudacris'
0.064130	0.128530	'Ambystoma_::Notophthal'
0.000010	0.080930	'Notophthal'
0.014720	0.089280	'Ambystoma_'
0.073290	0.280630	'Protopteru'
0.005400	0.032650	'Danio_reri::Leucoraja_::Oreochromi'
0.040030	0.216950	'Danio_reri::Oreochromi'
0.049640	0.209650	'Oreochromi'
0.055570	0.209500	'Danio_reri'
0.114780	0.402470	'Leucoraja_'
0.000000	0.000000	'Latimeria_'

test/G12210-O-S-1-NO.ref-tre  view on Meta::CPAN 

(((((((((Emys_orbic:0.023040,Chelonoidi:0.022240):0.017400,Pelodiscus:0.053490):0.044620,((Meleagris_:0.016820,Gallus_gal:0.009100):0.037590,Taeniopygi:0.057550):0.081090):0.014320,(Python_reg:0.107830,Anolis_car:0.097840):0.099780):0.033650,(((Loxod...

test/G12210-O-S-1-NO.tre  view on Meta::CPAN 

(((((((((Emys_orbic:0.013210,Chelonoidi:0.014950):0.000010,Pelodiscus:0.044150):0.035770,((Meleagris_:0.017320,Gallus_gal:0.033180):0.006880,Taeniopygi:0.015650):0.012790):0.002460,(Python_reg:0.013120,Anolis_car:0.000010):0.056650):0.020470,(((Loxod...

test/GNTPAN19392.ali  view on Meta::CPAN 

>Canis familiaris@ENSCAFP00000032577
MPPKTKEKRKKTGAQKKKENAG***ADVEVKYAHRLAVMEKELLQDHLALRRDEARRAKASEDQLRWRLQVLEAELEEARSEGKAIYAEMCRQCRALQKEMETHRRQQEEEVMGLRKKLEMCQREAEAAQQEAERALGERDQTLAQLRAHVVDMEAKYEEILHGNLDQLLAKLRAVRPQWDGAVLRLHAKYKEQLHQFGLNP********LDL
>Danio rerio@ENSDARP00000103065
MPPKKKGKGGSKKEKTKKSTPE***KDDGLTEKYRRSVLDVSVLKEHLALRSGVARQATAVRDELKSQVRDLEQLLSQERSDMKDITADLNRQYKSMETDLQSKADKLEASVDLLEKQLAECQVELKSERELRENTEAEKDAIISDLQSKLDSMERECEKILHGCLDSLLSHLADTRMKWEEQSTVIHQDVKDMLREFGINP********LHM
>Gallus gallus@ENSGALP00000033751
MPPKGKGKKKKAVKQHKKGKAA***AESQAAATSRSAALEADGLQEHPGHWRDVAWQARADSEGFQRRLWDLEQALEQAQDDKRDMHEEMTRQYQELQKQTAAHSQRLEAKVKSLQEQLATRLQETQHTQQAATKALAERDRTIAQLQSRMDTMQREYEKIFHDSLDLVLAKVADARQHWEEEGTTICLENKQRLQEFGLNP********LEI
>Homo sapiens@ENSP00000445431
MPPKNKEKGKKSGAQKKKKNWG***ADVVAESRHRLVVLEKELLRDHLALRRDEARRAKASEDQLRQRLQGVEAELEGARSEGKAIYAEMSRQCHALQEDMQTRSKQLEEEVKGLRGQLEACQREAAAAREEAEQALGERDQALAQLRAHMADMEAKYEEILHDSLDRLLAKLRAIKQQWDGAALRLHARHKEQQRQFGLTPPGSLRPPAPSL
>Loxodonta africana@ENSLAFP00000010014
MPPKTKEKG****AQKKKKNSSAGEADVEPESRHRLAMLEKELLRDHLALRRDEARQAKASEDQLKKRLQGLEAELEGARSEGKAIYAEMSRQHRALQEEMDTRSRQLEEEVRGLREQLETSKREAEAARRAAEQALRERDQMLAQLQAHVADMEAKYEEILHGSLNQLLAKLRAIKPQWDEAALRLHARHKEQLRQFGLNP********LDL
>Latimeria chalumnae@ENSLACP00000020224
MPPKKRAKGKKKKGKKKPVDDQ*HELDNAVEEKYKKASLEVEVLKDHLALRRNMCREAQACKEGLKLKLLTLERDLEDERDDKMVINADMTRQYKTMQTDMGIQVHQLEIEVSRLRQQLATCQQELQTTCEEKAWIVKEKDEMIIELQGKIDNMETEYEKILHESLDTLLAKLETAKFRWNDQATALHFQYKQKLLDFGLNP********LDI
>Monodelphis domestica@ENSMODP00000016556
MPPKIKRTGSKTGGQKKKKKSQ*GEADAETEIKHRRTALELEILRDHLALRRDETRQAIVCKERLQQRLQELEAEVERAQNDGKAVYAEMSRQYQALRKETETQSHRWEEEVKVLRKQLETCQREAKVAQGEAKQALAKRDKTLVQLQTYVTDMEAKYEEILHCSLDRLLAKLTIAKVEWDAATLRLHDKHKELLRQFGLNP********LDL
>Mus musculus@ENSMUSP00000090082
MPPKTKGRGRKAEARKKKKNSS***PGVEAEAKHRLVLLEKELLQDRLALQREEARRAKASEDRLKQRLQGLEAELERTQSEGKAIYAEMSRQRQALKEELGTRSKQLEEEVRSLKEQLETCQREAKTAKEEAERALRKQDGTLAQLHAHVADMEAKYEEILHDNLDCLLAKLRVVKPHWDANVLRLHTRLKEQLRQFGLNP********LDL
>Oreochromis niloticus@ENSONIP00000007825
MAPKKKTKKAAEKNPEK********CQNDVEEKRRHSILDIAILQDHIALQCEALRRVQSERADLRRRARDMEQKLQHERQDHRDIYWDLSRQYKTMQTKLTNKVKKLEQEVSQLKEDLALSQEELTKEKSERKQVEQEKDAIIADLRQKLDNIESDYEKILHETLDSLSSQLSLTRRGWEDESATLHQKYKEPLSEFGLNA********LDL
>Protopterus annectens@comp63786_c0_seq1
MPPKKKGKGKKKGKKKKSSD******ENVIEEKFKKASHEVDVLKDHLALRRDLVRQAQANNEEFKLKMLTLEKELDEERGEKKAISSDLTRQYKTLQADMVLRIHKLQTEVSHLQQQLESCREELKATQDEKERLVLEKDEVIAELQNKIDNMETDYERILHDGLDKLQSKIAAAKLQWEQQATTIHFEQKRLLLDFGLNP********LDI
>Xenopus tropicalis@ENSXETP00000053078

test/GNTPAN19590.ali  view on Meta::CPAN 

#
#
>Canis familiaris@ENSCAFP00000022865
*********************************************************************************************************************************************************TVTNAFILSLSLSDLLTALLCLPAAFLDLFTPP****PG****GSVGPWRGFCAASRFFSSCFGIVSTLSVALVSLDRYCAIVRPPREKLGRRRALQ...
>Homo sapiens@ENSP00000378548
M*EEPQPP*RPPASMALLGSQHSGAPSAAGPPGGTSSAAT**AAVLSFST*VATAALGNLSDASGGGTAAAPG**********GGGLGGSGAAREAGAAVRRP***LGPEAAPLLSHGAAVAAQALVLLLIFLLSSLGNCAVMGVIVKHRQLRTVTNAFILSLSLSDLLTALLCLPAAFLDLFTPPGGSAPA****AAAGPWRGFCAASRFFSSCFGIVSTLSVALISLDRYCAIVRPPREKIGRRRALQ...
>Loxodonta africana@ENSLAFP00000027579
**TDSRPPRGPMVTTSLLGSPQPDAPSAAGAPGGTSR*SF**STLATAAT*AAAAALGNQSDGSGGGTAAAP****************************RPP***LGPEAVQLLSHGAVVAAQALVLLLIFLLSSLGNCAVMGVIVKHRQLRTVTNSFILSLSLSDLLTALLCLPAAFLDLFTPPGGSAPAAATAASMGPWRGFCAASRFFSSCFGIVSTFSVALISLDRYCAIVRPPREKIGRRRALQ...
>Latimeria chalumnae@ENSLACP00000003015
***************************************************************************************************************************************************************************************************************ANGFFNSCFGIISTL**TLISFDRYYAVVRQPQEKIGKKQAIQ...
>Monodelphis domestica@ENSMODP00000032414
****************************SGASAGVGRGASFHAAVISFTTVAAVAAEARASRGGGGG*SGLAG**********AEKAGTGSTIHSNSSI***PVPAGAGAKRLLLEPWVAVAVQALVLLLIFLLSSLGNCAVMGVIVKHRQLRTVTNAFILSLSLSDLLTALLCLPAAFLALFTRPGGGSNG***PPIARPWQRFCTASRFFGSCFGIVSILTMTLISLDRYYAIVRHPGEKIGWHRALQ...
>Macropus eugenii@ENSMEUP00000010418
MEEEPPPP*PPRPPMSTRGSLRPEAALASGSSSGAARAAT**TAVISFTTAAAVAAEARASRGGGGGTAAAAG**********WGRVGSEATPAAAAAAQQQPVPEATGAKRLLLEPWAAVAAQALVLLFIFLLSSLGNCAVMGVIAKHRQLRTVTNAFILSLSLSDLLTALLCLPAAFLALFTPHAPAA*******AARPWQRFCTASRFFGSCFGIVSTLTMTLISLDRYNAIVRHPGGKLGWRRALL...
>Mus musculus@ENSMUSP00000058762
MEEQARPPGRPAASATLQGSAH*********PGGAASTAT**AAALSFSS*VATVTLGNQSD*AGRPEAAGS****************************RGP********APLLWHGAAVAAQALVLLLIFLLSSLGNCAVMGVIVKHRQLRTVTNAFILSLSLSDLLTALLCLPAAFLDLFAPPGDS**********GPWRSFCAASRFFSSCFGIVSTFSVALISLDRYCAIVRPPRDKLGRRRALQ...
>Oreochromis niloticus@ENSONIP00000025824
***************************************************MVTNLMATTTE*****TIVQTPGNLSDHKDQRGSEF********GHTHQELNPSVLSADESNSVLQGIIVAAQALILLSVFLLSSLGNSAVVIIIIKHRQLRTVTNAFIMSLSLSDFLTAVLCLPFSFVMLFTKDGVWMFG**********DRFCVANGCLNTCFGIISTLTMTLISFDRYYSIVRQPQAKIGRQKAAQ...
>Protopterus annectens@comp102315_c0_seq1

test/GNTPAN19593.ali  view on Meta::CPAN 

#
#
>Canis familiaris@ENSCAFP00000029981
******ENSGAPGTLPGPGGAKAAGGHRGEVKASAFSPGGQRLLTASEDGGGMAGRPGVG*LLWRLSGHTGPVKVCRFSLDGRLFATTSCDYTIRLWDTAEA*KCLHVLKGHQRSVGTVSFSPDSTQLASGGWDKR*MLWEVQSGQM**LHHLGGHRDSVQSSDFAPSSDSLATGSWDSTISIWDLRMATPVIFHQELEGHSGNISCLCYSASGLLASGSWDKTIHIWKPSTRSLLVQLKGHVTWVKSIA...
>Danio rerio@ENSDARP00000065847
******MWKRHPSEDFSVDNIRYFSRHKGEVNCCAFSPDCQLLLTCCDAGKLYLWKTSTAKLLASVSGHTGPVKCCVFSSDGRLFASASHDCSVRIWCSSSL*KCTHTLTAHRRSVETVSFSPDGQWLLSGGWDNRALIWSIQSGAL**LEELKGHNAAVQSSVFSSDSQSVATGSWDRAVRVWKLRDRQ**AEAMVLQGHLGNVACLCFSVAGML**********************************...
>Homo sapiens@ENSP00000362677
******MNSGVPATL*AVRRVKFFGQHGGEVNSSAFSPDGQMLLTGSEDGCVYGWETRSGQLLWRLGGHTGPVKFCRFSPDGHLFASASCDCTVRLWDVARA*KCLRVLKGHQRSVETVSFSPDSRQLASGGWDKRVMLWDVQSGQM**LRLLVGHRDSIQSSDFSPTVNCLATGSWDSTVHIWDLRMVTPAVSHQALEGHSANISCLCYSASGLLASGSWDKTIHIWKPTTSSLLIQLKGHVTWVKSIA...
>Loxodonta africana@ENSLAFP00000008398
AGWPGPMNNRAPGTL*AVGRVKYFGRHHGEVNSSAFSPNGQTLLTASDDGCVYGWETQTGQLLWKLGGHTGAVKFCRFSPDGRLFASTSCDCTIRLWDVARA*KCLQVLKGHQRSVETVSFSPDSRQLASGGWDKRVMLWEVQTGSRLFLHSFVLLAQTLLWFRFSPSADCLATGSWDSTVRIWDLRAGTPKTFHHKLEGHSGNISCVCYSPSGLLASGSWDKTIRIWKPQPASLLVQLKGHVTWVKSIA...
>Latimeria chalumnae@ENSLACP00000020944
*******MWRNPIESFVITNIKYFPEHKGEVNSCAFSPDCQILLACSDDNRVYVWNVKTQKLICKVKGHTGPVNACAFSPDCSIFASASHDCTVRVWKTATT*ECLHVLKDHLKSVETVCFNPDSRQLLSAGWDYTAILWDAQLGLN**LKTFYGHQDVIQSSAFSLNGQFLATGSWDYTAKLWNLRKDE***PEKTLEGHKGNVSCVCFSVSGMLATGSWDRTVRVWNPKKGVLIFLLEGHSGWVKSVA...
>Monodelphis domestica@ENSMODP00000024654
*********KSWAPL*TVGSVKYYSRHKGEVNSCAFSPDTRILLTCCDDNQVYMWESRSGRLLRKLQGHTGPVRFCKFSPNGKYFASASRDCTVRLWDAKTSIICLHVLKGHSRSVETVSFSSNSKRLVSGGWDHKAILWDVKKGQM**ITELLGHHDAIQSSDFSSVSEYLATGSWDSTVQVWDLSILG*NIRKKTLEGHEGNVSCVCFSPSGLLASGSWDKTIRIWNPETGKLLIQLLGHLTWVKSMA...
>Macropus eugenii@ENSMEUP00000006091
******************************VNSCAFSPDTRILLTCCDDNKVYMWGARTGNLLRKLQGHKGPVSFCRFSPDGKFFASASRDCTVRLWDAQTT*KCLQVLKGHSRGVETVSFSSDSKQLASGGWDRKAILWEVQ***********GHRDAIQSSDFSPSSEYLATGSWDSTVQVWDLRAIR**LKKKILEGHKGNVSCVCFSPSGLLASGSWDKTICIWKPETGKLLSKLLGHLTWVKSMA...
>Mus musculus@ENSMUSP00000043834
MEW*APMNIRAPTRL*AVGRVRFYGQHHGEVNCSAFSPDGRTLLTASDDGCVYVWGTKSGRLLWRLAGHRGPVKSCCFSPDGRLIASSSSDHSIRLWDVARS*KCLHVLKGHQRSVETVSFSPDSKQLASGGWDKRAIVWEVQSGRR**VHLLVGHCDSIQSSDFSPTSDSLATGSWDSTVHIWDLRASTPVVSYHNLEGHTGNISCLCYSASGLLASGSWDKTICVWKPTTNNLPLQLKGHTIWVNSLA...
>Protopterus annectens@comp482267_c0_seq1
*********************************************************************************************ARVWKTSTA*ECLHILKGHSKIVETVCFSPDSRQLLTGGWDCTAILWDVQSGHH**MKTFYGHESAIQCSAFAPNGQYLATGSWDYTVKIWDLLKEG***KEKTLNGHRGNISCVSFSKLGMLASSSWDKTVRVWNPKSEALIFLLNGHSGWVKSLA...
>Xenopus tropicalis@ENSXETP00000036715

test/GNTPAN19618.ali  view on Meta::CPAN 

#
#
>Canis familiaris@ENSCAFP00000014630
************************MGCGPSQAAED**QRR*VPAPRKGWEEGFKA******DIPV**THSGEGCRPQDEAAFPKDSRSSPNGLE***NLGSLPGTIPESSPSLSER*****NGRINS*DLVTSGLIHKPQPLESRE******RQKSSDILEELIVQGII***QSHSKVFRNGESYDVMVSTT*MPLRKPPARLKKLTIK*KEAKAFTMNDLEEKMRAVESRRKTKEEDIRKRLR**SDRL...
>Danio rerio@ENSDARP00000102039
MRMIEEVYPDPRTSEEPHNQRETNMGCGSSRITVV**EP**VKTSNL****NGNETDTLQFDVA********QGGSRGDSAISKMTIDSGVSLDAAEA*AGLPGTVPRLLPQLQAQ***********************TPGHSEE******RPESSEILEQLLAQGII***PAQPKHGESGQSYNIMMDDTGKARSRPPARLESLKTR*KEQEITKKEDIEMKMRLVEERRKEREEDLKRRLRIKSARP...
>Homo sapiens@ENSP00000455698
************************MGCGPSQPAED**RRR*VRAPKKGWKEEFKA******DVSV**PHTGENCSPRMEAALTKNTVDIAEGLEQ*VQMGSLPGTISENSPSPSER*****NRRVNS*DLVTNGLINKPQSLESRE******RQKSSDILEELIVQGII***QSHSKVFRNGESYDVTLTTTEKPLRKPPSRLKKLKIK*KQVKDFTMKDIEEKMEAAEERRKTKEEEIRKRLR**SDRL...
>Loxodonta africana@ENSLAFP00000026635
**************************CNPSNGRRDQYLVE*ILSLTKPFLPFPQA******DVGE**THSEDNCRPQIKAPLPKDTADSAEGLEKRAQMGSLPGTIPESSPSPSEQ*****NGRVHSEDLVPNGLISKPQDLENRE******RQRSSDILEELIVQGII***QSHSKVFRNGESYDVMVDTTEKPLRKPPARLKKLKIK*REVKDFTMKDIEEKMQAVEERRKTKEEEIRKRLR**SDRP...
>Latimeria chalumnae@ENSLACP00000022722
************************MGCGSSRTIVV**QP**VNGIK*****NGRPRGENNNEVKQSPSGTSITSNARDGSAVSKHTTDSGVEIDELAA*GNLPGVVPKRLKPLKEKVGPLPSNEMNIDLPVNRSGLNQKNRQDLRG******RQNSTDILEELLMQGII***QSRSRIVRNGEAFDVM*********************************************SKEEELKKRLR**SERP...
>Monodelphis domestica@ENSMODP00000013630
************************MGCGASKPVEG**QRP*VPEPKKGWEEGSKV******VIGE**SRISVDVEPWNGSARPKSTTDSGVGLEERVLMESLPGTIPENSLSLDER*****NEEVNT*EPVISGLINTSQHLQSQE******RLKSSDILEELIIQGII***QSQSKVFRNGESYNMNMD**EKPLRKPPARLEKLKTK*RETNGFTIKNIEEKMKAADERRKVKGEEMKKRLR**SDRP...
>Mus musculus@ENSMUSP00000075923
************************MGCGPSQQKEDQSQSR*IPSPRKGWEEGSKA******DVRV**TSSKENCSPQTEAAWPKHTIDNAKSLDQQAQIGSLPGTIPENSPTPSKT*****SRRINS*DPVANGLTNKPQLPESWE******RPKSSDILEELIVQGII***QSRSKVFRNGESYDVMVDTTEKPLRKPPARLKKLKVK*KEVKDFTIQDIEEKMQAAEERRKTKKEEIRKRLR**SDRL...
>Xenopus tropicalis@ENSXETP00000062379
**********************LSMGCKNSRIQVV**QP**TDGRTSGWGSNGKVQPESQDDIK***ANNNNSSNARDGSALSKGTMDSGLGLEDESS*GALPGTVTEKLPSP********RGRLNNDLPLLNS*****GRGTPRE******RQTSSDILEELMTQGII***QSQAKVVRNGEAFDVLMDTPEKPLRRPPAKLEKLQTKQKKKKNLTREDIENKMKAVEERRKTKEEELKKRLR**SERP...
>Oreochromis niloticus@ENSONIP00000003137
**********************VKMGCLNSTITTV**QTLTVNGDEVGWVSHHPLCLCCQDD*******TGSKLSGRGDSAVSKGTADSGVVMENR***GDIPGAVPRTLPPLTSE*****SIRENVLL**********RDNEITE******RQNSHKILEELLNQGIIPKEQHREKSSRVGEAYSIMLDDNEGARRRPPARLESLKMK*KAQILHTREELEEKIRLAEERRKLKEDKLKMRLRTKSARI...
>Protopterus annectens@comp49672_c0_seq1

test/GNTPAN19639.ali  view on Meta::CPAN 

#
#
>Canis familiaris@ENSCAFP00000029023
MPKSCAARQCCNRYSSRRKQLTFHRFPFSRPELLKEWVLNIGRANFKPKQHTVICSEHFRPECFSAFGNRKNLKQNAVPTVFAFQDATQLARENADPAGGDTNVDSHNRPQVASEVVPAECGWGRKLEAALE**VLPPMASGPAEQVVPRR**LQGTQAPAQ*QASP******SPAQTSDHSYALLDLDALKKKLFLTLKENEKLRKRLKAQRLVIRRMSSRLRAHRAGPP*******************...
>Homo sapiens@ENSP00000054650
MPKSCAARQCCNRYSSRRKQLTFHRFPFSRPELLKEWVLNIGRGNFKPKQHTVICSEHFRPECFSAFGNRKNLKHNAVPTVFAFQDPTQQVRENTDPASERGNASSSQKEKVLPEAGAGEDSPGRNMDTALEELQLPPNAEGHVKQVSPRR**PQATEAVGR*PTGPAGLRRTPNKQPSDHSYALLDLDSLKKKLFLTLKENEKLRKRLQAQRLVMRRMSSRLRACK*GHQGLQA***************...
>Loxodonta africana@ENSLAFP00000013404
MPKSCAARQCCNRYSNRRKQLTFHRFPFSRPELLKEWVLNIGRGNFKPKQHTVICSEHFRPECFSAFGNRKNLKHNAVPTVFAFQDPTQ**********************VLPMAGV**DGTGRSMDTTLDELQVPPNAEAPGKEVLPYR**LEAAEAPAR*PASPMGLKQSLPKQPSDHSYALLDLDALKKKLFLTLKENEKLRKRLRAQRLEMRRMCRRLSARREGRQRAQA***************...
>Latimeria chalumnae@ENSLACP00000017875
MPKSCAALDCRSRYSNKNKELTFHRFPFSKPDLLKEWMENIGRVDFEPKQHTVICSKHFKPECFNKFGNRKNLNHNAVPTIFT***SSRLAKESS*ASETISNQETRTP*********ALEMVLMQEGPLLVVPELAATVEVDDTN*******LKPLQAAYNLQEPPLSGRAS****DPDHNYALKSSASLKRRLFLTLEENEKLQKRLKLKTEGLRRITLKLHEVKRELDKLRGGHKPPLTTTKSPHVS...
>Monodelphis domestica@ENSMODP00000007324
MPKSCAARQCCNRYSSRRKQLTFHRFPFSRPELLKEWVLNIGRGNFKPKQHTVICSEHFKPDCFSAFGNRKNLKQNAVPTVFAFQETAQLVRENTDPAAERSDAQAQQLGKDFSGAGAREYTPGRKMEIPLDKHQLSPDAEASEKEVSSYR**TEEAESHLL*PTCPTGQKGSLSLPESDHSYALLDLDALKKKLVLTLKENERLRKRLKLQRVAMRRMSSRLQALQEEKRRQKA***************...
>Macropus eugenii@ENSMEUP00000001866
*************************FPFSRPELLKEWVLNIGRGNFKPKQHTVICSEHFKPDCFSAFGNRKNLKQNAVPTVFAFQDTAQLVRENTDPAGQRSD********DFSDAGAGEYTSGRKMEHPLDKPQLPPEAEASEKE***************L*PPSPLGQRGSLSLPASDHSYALLDLDALKKKLVLTLKENERLRRRLKMQRVAMKRMSSRLQALQEEKR*******************...
>Mus musculus@ENSMUSP00000035240
MPKSCAARQCCNRYSSRRKQLTFHRFPFSRPELLREWVLNIGRADFKPKQHTVICSEHFRPECFSAFGNRKNLKHNAVPTVFAFQNPTE**********************VCPEVGAGGDSSGRNMDTTLEELQ*PPTPEGPVQQVLPDREAMEATEAAGL*PASPLGLKRPLPGQPSDHSYALSDLDTLKKKLFLTLKENKRLRKRLKAQRLLLRRTCGRLRAYREGQPGPRA***************...
>Protopterus annectens@comp33466_c0_seq1
MPKSCAALRCGNRYNSKNKDLTFHRFPFSKPELLKEWLENVGREDFTPKLHTVICSKHFKPECFSPFGNRKNLKHNAVPTIFNN*****CLEKAKDPNAFPSHHPVLEP***********NSATVEIVVELEDDSTCPQVGINKN***********MEMATQITQSACALRQQISVPTMDHSYAIKDCNLLKKQFFQMLEQNKRLRKQIKMKTKEIRRMSATLWVVKNELRQLKA***************...
>Dasypus novemcinctus@ENSDNOP00000010734

test/GNTPAN19649.ali  view on Meta::CPAN 

>Canis familiaris@ENSCAFP00000035432
M*******************ALPSKAVIVPGNGGGDVATHGWYGWVKKGLEQNKIPGLCLKTKCLAKNMPDPITARESLWLPFMETELHCDEKTVIIGHSSGAIAAMRYAETHRVYAIVLVSAYTSDLGDENEQASGYFNRPWQWERIKANCPHIVQFGSTDDPFLPWKEQQEVADRLEAKLYKFTDRGHFQNMEFHELIRVIKSMLKVPA
>Dasypus novemcinctus@ENSDNOP00000008316
M*******************ASPSKAVIVPGNGGGDVATHGWYGWVKRGLE**QIPGF****QCLAKNMPDPIMARESIWLPFMETELHCDDRTIVIGHSSGAIAAMRYAETHRVYAIILVAAYTSDLGDENECASGYFNRPWQWEKIKANCPHIVQFGSTDDPFLPWKEQQEVADRLEAKLHKFTDRGHFQNTEFHELISVVKSMLKVPA
>Danio rerio@ENSDARP00000095196
M********************PLKRVVIVPGNGAGDVERSNWYGWANKRIN**EIPDL****SCALKNMPDPVTARESVWLPFMEKDLKCDEETLIIGHSSGAAAAMRYAETHKVFAIILVGAYTSHLGDENERESGYFSRPWEWEKIRANVEYILQFGSTDDPFLPWDEQQEVADGLKTDLHKYSDRGHFQNTAFPELIDAVNKLKTN*S
>Homo sapiens@ENSP00000336866
M*******************ASPSKAVIVPGNGGGDVTTHGWYGWVKKELE**KIPGF****QCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTDCGHFQNTEFHELITVVKSLLKVPA
>Loxodonta africana@ENSLAFP00000001073
M*******************ASPSKAVIVPGNGGGDVATHGWYGWVRKRLE**RIPGF****QCLAKNMPDPITAQESIWLPFMETELHCDEKTIVIGHSSGAIAAMRYAETRRVYAIVLVSAYTSDLGDENERASGYFSRPWQWEKIKANCSHIVQFGSTDDPFLPWKEQQEVADKLEAKLYKFTDRGHFQNTEFHELISVVKSMLKVPA
>Latimeria chalumnae@ENSLACP00000010432
HCSCGPRKLHEFFADLLGYNMSPLKAVIVPGNGGGNVEYCNWYGWAKKQLN**KVPNF****QCLLKNMPDPITARESIWLPFMESELKCDEETVIIGHSSGAAAAMRYAETHKVYAIVLVSAYTSDLGDANERESGYFSRPWQWENIKSNCCCIVQFGSTDDPFLPWKEQQEAADGLGAELHKFTDKGHFQNTEFSELIDVVQKMLTT*T
>Monodelphis domestica@ENSMODP00000006991
M*******************VSPSKAVIVPGNGGGDVVTHGWYGWVKKRLE**KIPDF****QCLSQNMPDPIIARESIWLPFMESEFHCDEKTIIIGHSSGAIAAMRYAETHRVYAIILVSAYTSDLGDENERASGYFNRPWQWEKIKSNCQHIVQFGSTDDPFLPWSEQQEVANELGAKLHKFTDRGHFQNTEFNELVNVVQSMLNVPA
>Macropus eugenii@ENSMEUP00000011272
M*******************VSPSKAVIVPGNGGGNVVTHGWYGWVKKRLE**EIPNF****QCLSQNMPDPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYAETHRVYAIILVSAYTSDLGDXXXXXXXYFNRPWQWEKIKSNCQHIVQFGSTDDPFLPWSEQQEVADELGAKLHKFTDRGHFQNTEFSELVSVVQSMLNVPA
>Mus musculus@ENSMUSP00000028915
M*******************ASPNKAVIVPGNGGGDVATHGWYGWVKKGLE**QIPGF****QCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHQVYALVLVSAYTSDLGDENERASGYFSRPWQWEKIKANCPHIVQFGSTDDPFLPWKEQQEVADRLDAKLYKFTDRGHFQNTEFHELISVVKSMLKGPE
>Protopterus annectens@comp13196_c0_seq1
M**************SVDKIFPATKAVIVPGNGGGSVEYCNWYGWTRKALN**KIPNF****QCYLRDMPDPMTARESIWLPFMESELQCDERTVIIGHSSGAAAAMRYAETHKVYAIILVSAYTSDLGDDNERESGYFNRSWQWEKIKSNCKHIIQFGSTDDPFLPWSEQQEVVDKLGAVLHKYQDRGHFQNTQFHELVSAVQDLLQESQ

test/classifier.yaml  view on Meta::CPAN 

categories:
- label: strict
  description: strict species sampling
  criteria:
  - tax_filter: [ +Latimeria ]
    min_seq_count: 1
    max_seq_count: 
    min_org_count:
    max_org_count: 
    min_copy_mean: 
    max_copy_mean: 
  - tax_filter: [ +Protopterus ]
  # min_seq_count defaults to 1
  # max_seq_count defaults to no upper bound
  # all other also default to no bound
  - tax_filter: [ +Danio, +Oreochromis ]
  - tax_filter: [ +Xenopus ]
  - tax_filter: [ +Anolis, +Gallus, +Meleagris, +Taeniopygia ]
  - tax_filter: [ +Mammalia ]
- label: loose
  description: loose species sampling
  criteria:
  - tax_filter: [ +Latimeria ]
  - tax_filter: [ +Protopterus ]
  - tax_filter: [ +Danio, +Oreochromis ]
  - tax_filter: [ +Amphibia, +Amniota ]

test/speclist.idm  view on Meta::CPAN 

Danio rerio	Drer
Dasypus novemcinctus	Dnov
Discoglossus pictus	Dpic
Elaphe guttata	Egut
Emys orbicularis	Eorb
Eublepharis macularius	Emac
Gallus gallus	Ggal
Homo sapiens	Hsap
Hymenochirus curtipes	Hcur
Lampropholis coggeri	Lcog
Latimeria chalumnae	Lcha
Lepisosteus oculatus	Locu
Leucoraja erinacea	Leri
Loxodonta africana	Lafr
Macropus eugenii	Meug
Meleagris gallopavo	Mgal
Monodelphis domestica	Mdom
Mus musculus	Mmus
Notophthalmus viridescens	Nvir
Oreochromis niloticus	Onil
Ornithorhynchus anatinus	Oana



( run in 0.416 second using v1.01-cache-2.11-cpan-87723dcf8b7 )