Bio-MUST-Core

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

# amino-acids sequences. (...) The maximum number of characters in species
# name MUST not exceed 100. Blanks and the symbols "(),:" are not allowed
# within sequence names because the Newick tree format makes special use of
# these symbols. However, blanks (one or more) MUST appear at the end of each
# species name.

# TREE-FINDER: http://www.treefinder.de/tf-march2011-manual.pdf
# A sequence name may consist of 1 to 10 alphanumeric characters, dashes "-",
# dots ".", underscores "_", or some of "/", "?", "*", "+". No space is
# allowed inside the names. The first name character must be a letter or an
# underscore. A sequence fragment may start behind position 10 after a
# sequence name, or anywhere in a line without a name.

# TREE-PUZZLE [data/globin.a]
#   7 128
# HBB_HUMAN      HLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFDLSMGN
# HBB_HORSE      QLSGEEKAAV LALWDKVNEE EVGGEALGRL LVVYPWTQRF FDSFDLSMGN
# HBA_HUMAN      VLSPADKTNV KAAWGKVGAG EYGAEALERM FLSFPTTKTY FPHFDLSHGS
# HBA_HORSE      VLSAADKTNV KAAWSKVGAG EYGAEALERM FLGFPTTKTY FPHFDLSHGS
# MYG_PHYCA      VLSEGEWQLV LHVWAKVEVA GHGQDILIRL FKSHPETLEK FDRFHLKKAS
# GLB5_PETMA     PLSAAEKTKI RSAWAPVYYE TSGVDILVKF FTSTPAAQEF FPKFGLTKKS

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

    DB_16s_F8
    DB_16s_R8
    debontii_A
    debontii_B
    debontii_C
    defectiva_A
    defensa_A
    defluvii_A
    defluvii_B
    defluvii_C
    defragrans_A
    dehalogenans_B
    delafieldii_A
    delafieldii_B
    delafieldii_C
    delaneyi_A
    delbrueckii_B
    deleyi_A
    deleyi_B
    dendritiformis_A
    dendritiformis_C

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

    formigenes_C
    formigenes_D
    formigenes_E
    formosense_A
    formosum_A
    forsythia_A
    fortis_A
    FR1_11-MR-2014
    FR1_16_MR-2014
    FR3_2_MR-2014
    fragariae_A
    fragi_D
    fragilis_A
    fragilis_B
    frankenforstense_A
    franklandus_A
    frederiksbergense_A
    frederiksbergense_B
    frederiksbergensis_A
    frederiksbergensis_B
    frederiksbergensis_D
    frederiksbergensis_F
    frederiksbergensis_G
    frederiksbergensis_H

test/OG0000464-edit-MMETSP172.idm  view on Meta::CPAN

Cyclotella meneghiniana_29205@MMETSP1057-DN7396_c1_g1_i2#NEW#	seq596
Cylindrotheca closterium_2856@MMETSP0017-DN27_c0_g1_i1#NEW#	seq597
Cylindrotheca closterium_2856@MMETSP0017-DN1804_c0_g1_i1#NEW#	seq598
Cylindrotheca closterium_2856@MMETSP0017-DN2481_c0_g1_i1#NEW#	seq599
Cylindrotheca closterium_2856@MMETSP0017-DN12262_c0_g1_i2#NEW#	seq600
Cylindrotheca closterium_2856@MMETSP0017-DN14915_c0_g1_i4#NEW#	seq601
Cylindrotheca closterium_2856@MMETSP0017-DN14915_c0_g1_i5#NEW#	seq602
Cylindrotheca closterium_2856@MMETSP0017-DN14915_c0_g1_i7#NEW#	seq603
Cylindrotheca closterium_2856@MMETSP0017-DN17411_c0_g1_i1...Euglena_gracilis#NEW#	seq604
Cylindrotheca closterium_2856@MMETSP0017-DN17802_c0_g1_i1+1#NEW#	seq605
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN1810_c0_g1_i1#NEW#	seq606
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN6685_c0_g1_i1...Prymnesiophyceae#NEW#	seq607
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN6685_c0_g2_i1...Prymnesiophyceae#NEW#	seq608
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN6685_c2_g1_i1...Prymnesiophyceae#NEW#	seq609
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN6685_c3_g1_i1...Isochrysidales#NEW#	seq610
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN7428_c0_g1_i1#NEW#	seq611
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN7428_c0_g1_i2#NEW#	seq612
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN8012_c10_g2_i1...Sar#NEW#	seq613
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN8012_c10_g2_i2#NEW#	seq614
Dactyliosolen fragilissimus_1118495@MMETSP0580-DN8012_c10_g2_i5#NEW#	seq615
Detonula confervacea_83371@MMETSP1058-DN1776_c0_g1_i1#NEW#	seq616
Detonula confervacea_83371@MMETSP1058-DN7255_c0_g1_i1#NEW#	seq617
Detonula confervacea_83371@MMETSP1058-DN8737_c2_g1_i1#NEW#	seq618
Detonula confervacea_83371@MMETSP1058-DN9155_c5_g1_i1#NEW#	seq619
Dictyocha speculum_35687@MMETSP1174-DN26406_c0_g1_i1#NEW#	seq620
Dictyocha speculum_35687@MMETSP1174-DN26706_c1_g1_i1#NEW#	seq621
Dictyocha speculum_35687@MMETSP1174-DN26706_c1_g1_i2#NEW#	seq622
Dictyocha speculum_35687@MMETSP1174-DN26706_c1_g1_i3#NEW#	seq623
Dictyocha speculum_35687@MMETSP1174-DN26706_c1_g1_i4#NEW#	seq624
Dinobryon sp._98059@MMETSP0019-DN1459_c0_g1_i1...Eukaryota#NEW#	seq625