BioPerl

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t/LocalDB/Taxonomy/silva.t  view on Meta::CPAN

# each_Descendent; must ask the database directly
@ids = $db->get_taxonid('Metazoa');
is scalar @ids, 1;
$id = $ids[0];
ok $node = $db->get_taxon($id);
ok @children = $node->db_handle->each_Descendent($node);
is scalar @children, 3; # Chordata, Platyhelminthes, Metazoa

# do some trickier things...
ok $node2 = $db->get_taxon('sv112');
is $node2->scientific_name, 'Mucoromycotina';

# briefly check that we can use some Tree methods
$tree = Bio::Tree::Tree->new();
is $tree->get_lca($node, $node2)->scientific_name, 'Eukaryota';

# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $node2);
is $tree->number_nodes, 5;
is $tree->get_nodes, 5;

t/data/Bird_Ovomucoids.nex  view on Meta::CPAN

Phalacrocorax_sulcirostris      .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S....   [86]
Anhinga_novaehollandeae         .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S....   [86]
Nycticorax_nycticorax           .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S....   [86]
Chauna_chavaria                 .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S....   [86]
Anseranas_semipalmata           .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S....   [86]
Dendrocygna_arcuata             .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S....   [86]
Dendrocygna_autumnalis          .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S....   [86]
Dendrocygna_eytoni_d            .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S....   [86]
Dendrocygna_eytoni_e            .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S....   [86]
Dendrocygna_viduata             .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S....   [86]
Coscoroba_coscoroba             ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S....   [86]
Cygnus_atratus                  .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S....   [86]
Goose                           .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....   [86]
Anser_indicus                   .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....   [86]
Branta_canadensis               .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S....   [86]
Cereopsis_novaehollandiae       ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S....   [86]
Chloephaga_picta                .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E   [86]
Duck                            .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E   [86]
Anas_platyrhynchos              .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E   [86]
Megapodius_freycinet            .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S....   [86]
Leipoa_ocellata                 IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S....   [86]

t/data/Bird_Ovomucoids.nex  view on Meta::CPAN

		11	Phalacrocorax_sulcirostris,
		12	Anhinga_novaehollandeae,
		13	Nycticorax_nycticorax,
		14	Chauna_chavaria,
		15	Anseranas_semipalmata,
		16	Dendrocygna_arcuata,
		17	Dendrocygna_autumnalis,
		18	Dendrocygna_eytoni_d,
		19	Dendrocygna_eytoni_e,
		20	Dendrocygna_viduata,
		21	Coscoroba_coscoroba,
		22	Cygnus_atratus,
		23	Goose,
		24	Anser_indicus,
		25	Branta_canadensis,
		26	Cereopsis_novaehollandiae,
		27	Chloephaga_picta,
		28	Duck,
		29	Anas_platyrhynchos,
		30	Megapodius_freycinet,
		31	Leipoa_ocellata,

t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta  view on Meta::CPAN

UGGCGAACGG GUGAGUAACG CGUAAGAACC U
>AACV01029078.1.1500 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
CCCUAUCAAC UUUCGAUGGU AGGAUAGGGG CUACCAUGGU GGUGACGGGU GACGGAGAAU UAGGGUUCGA UUCCGGAGAG
GGAGCCUGAG AAACGGCUAC CACAAUCCAA 
>AACV01032541.12.1684 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
ACUCGGAUAA CCGUAGUAAU UCUAGAGCUA UAGUGCAACA AACCCCGACU UCCGGGAGGG GCGCAUUUAU UAGAUAAAAG
GCUGACGCGG GCUCCGCCCG CUGAUCCGAU GAUUCAUGAU AACUCGACGG AUCGCACGGC CCUCGUGCCG GCGACGCAUC
AUUCAAAUUU CUGCCCUAUC AACUUUCGAU GGUAGGAUAG GGGCCUAC
>AACV01034311.49.1859 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
ACCUGGUUGA UCCUGCCAGU AGUCAUAUGC UUGUCUCAAA GAUUAAGCCC AUGCAUGUGC AAGUAUGAAC UAA
>AACW02000151.263262.264792 Eukaryota;Fungi;Fungi incertae sedis;Basal fungal lineages;Mucoromycotina;Mucorales;Mucoraceae;Rhizopus;;Rhizopus oryzae RA 99-880
ACUCGAUUUU CUGCCCUAUC AUGGUUGAGA UUGUAAGAUA GAGGCUUACA AUGCCUACAA CGGGUAACGG GGAAUUAGGG
UUCGAUUCCG GAGAGGGAGC CUGAGAAACG GCUACCACAU CCAAGGAAGG CAGCAGGCGC GCAAAUUACC CAAUCCCGAC
ACGGGGAGGU AGUGACAAUA CAUAACAAUG CAGGGCCUUU AAGGUCUUGC AAUUGGAAUG AGUACAAUUU
>AACY020014137.1.1251 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Cryomorphaceae;Owenweeksia;marine metagenome
CCAAGGCAAC GAUGUCUAGG GGUUCUGAGA GGAUGAUCCC CCACACUGGU ACUGAGACAC GGACCAGACU CCUACGGGAG
GCAGCAGUGA GGAAUAUUGC GCAAUGGAGG AAACUCUGAC GCAGCCA
>AACY020043159.616.2094 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;SAR116 clade;marine metagenome
UAAGAGUUUG AUCCUGGCUC AGAAUGAACG CUGGCGGCAU GCCUAACACA UGCAAGUCGA ACGAGAUCUU CGGAUCUAGU
GGCGCACGGG UGAGUAACGC GUGGGAACCU ACCUUUUAGU ACGGGACAAC GUUUGGAAAC GAACGCUAAU ACCGUAUACG
CCCUCCGGGG GAAAGGUCAG CCGCUAAA

t/data/tol-2010-02-18.nhx  view on Meta::CPAN

(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=5...