Bio-NEXUS

 view release on metacpan or  search on metacpan

t/charactersblock_methods-02.t  view on Meta::CPAN

	  	'states' => {
	    	'1' => 'out,_dorsal,_back', 
	  		'2' => 'out,_dorsal,_back,_ventral', 
	  		'3' => 'out,_dorsal,_back,_ventral,_second_turn' 
	  	}
	},
	{ 
		'id' => '3',
	  	'char_label' => 'P6.p_requirement_for_late_induction', 
	  	'states' => {
	    	'1' => 'not_required', 
	  		'2' => 'required', 
	  		'3' => '(not_applicable)' 
	  	}
	}	
];

#   	2  Dependence_on_gonadal_induction_before_VPCs_divide / no_gonad_requirement dependent_on_gonad,
#   	4  Source_of_first_induction_signal / gonad AC gonad_independent,
#   	8  'B: P5.pap/P7.ppa division' / U L T O,
#   	9  'C: P5.ppa/P7.pap division' / U L T,
#   	10  'D: P5.ppp/P7.paa division' / U L T,
#   	11  P4.p_lineage_pattern / 'S_(no_division)' 'SS_(1_division)' 'Sss_(2_divisions;_inner_daughter_divides_again)' 'SSSS_(3_divisions)' '(SSLL)_(5_divisions;_inner_granddaughters_divide_L)' 'LLLL_(7_divisions;_8_cells)',

t/data/compliant/04_characterstatelabels_05.nex  view on Meta::CPAN

	dimensions ntax=3;
	taxlabels taxon_1 taxon_2 taxon_3;
end;

['Characters' block from Maddison et al. 1997, p. 601 right column]

begin characters;
	dimensions nchar=3;
	charstatelabels 
	  1  DTC_migration_pattern / 'out,_dorsal,_back' 'out,_dorsal,_back,_ventral' 'out,_dorsal,_back,_ventral,_second_turn',
	3  P6.p_requirement_for_late_induction / not_required required '(not_applicable)',
  	2  Dependence_on_gonadal_induction_before_VPCs_divide / no_gonad_requirement dependent_on_gonad,
  	4  Source_of_first_induction_signal / gonad AC gonad_independent,
  	8  'B: P5.pap/P7.ppa division' / U L T O,
  	9  'C: P5.ppa/P7.pap division' / U L T,
  	10  'D: P5.ppp/P7.paa division' / U L T,
  	11  P4.p_lineage_pattern / 'S_(no_division)' 'SS_(1_division)' 'Sss_(2_divisions;_inner_daughter_divides_again)' 'SSSS_(3_divisions)' '(SSLL)_(5_divisions;_inner_granddaughters_divide_L)' 'LLLL_(7_divisions;_8_cells)',
  	12  P8.p_lineage_pattern / 'S_(no_division)' 'SS_(1_division)' 'ssS_(2_divisions)' 'SSSS_(3_divisions)' 'LLSS_(5_divisions)' 'LLLL_(7_divisions)',
  	20  P3.p_division_frequency / in_less_than_20%_of_cells more_than_20%_of_cells 
  	5  P6.p_lineage_pattern / TTTT TUUT UTTU UUTT UTTT,
  	6  'P (5,7).p lineage pattern' / UUUU LUUU LLUU LLLU LLTU LULU LOTU sUUU UULL,

t/data/compliant/Treebase-horsetails-classic.nex  view on Meta::CPAN

	39  'dichopodial' 'monopodial',
	40  'absent' 'present',
	41  'absent' 'present',
	42  'non-septate' 'septate',
	43  'undifferentiated' 'differentiated',
	44  'absent' 'present',
	45  '1-18' '1-6_(rarely_9)' '2.',
	46  'absent' 'present' 'present_with_septae',
	47  'parenchymatous' 'sclerenchymatous',
	48  'parenchymatous' 'sclerenchymatous',
	49  'not_differentiated' 'differentiated',
	50  'single_apical_cell' 'complex',
	51  'primary' 'secondary' 'tertiary',
	52  'absent' 'present',
	53  'scalariform' 'circular' 'conifer-type',
	54  'absent' 'present',
	55  'absent' 'present',
	56  'diameristic' 'parameristic' 'anomomeristic',
	57  'perigenous' 'mesogenous' 'mesoperigenous',
	58  'absent' 'present',
	59  'absent' 'present',

t/data/compliant/Treebase-horsetails-classic.nex  view on Meta::CPAN

	78  'continuous_bow' 'interrupted_bow' 'restricted_patch',
	79  'longitudinal' 'transverse',
	80  'ectokinetic' 'endokinetic',
	81  'homosporous' 'heterosporous',
	82  'absent' 'present',
	83  'present' 'absent',
	84  'monolete' 'tetrahedral' 'linear',
	85  'linear' 'triradiate' 'circular' 'sulcate',
	86  'absent' 'present',
	87  'absent' 'present',
	88  'not_prominent' 'prominent,_not_cavate' 'prominent,_cavate',
	89  '(nearly)_smooth' 'sculptured',
	90  '2-layers_(blechnoid)' '3-layers' '5-layers',
	91  '(nearly)_smooth' 'sculptured',
	92  'absent' 'present',
	93  'absent' 'present',
	94  'centripetal' 'centrifugal',
	95  'parietal' 'plasmodial',
	96  'maximum_size_in_water' 'maximum_size_in_sucrose_concentrations',
	97  'no' 'yes',
	98  'equatorial' 'polar' 'amorphous',

t/data/compliant/Treebase-horsetails-classic.nex  view on Meta::CPAN

	109  'absent' 'present',
	110  'absent' 'present',
	111  'blocks' 'random' 'single',
	112  'more_than_1000' '100-999' '16-64' '2-15',
	113  'absent' 'suspended' 'penetrating',
	114  'biflagellate' '3-20' '30-100' '1000-10000',
	115  'side_by_side' 'anterior-posterior' 'continuous',
	116  'absent' 'present',
	117  'sperm_mother_cell' 'sperm_mother_cell_progenitor',
	118  'absent' 'present',
	119  'paired' 'not_paired',
	120  '5_or_more' '4.' '3.',
	121  'embedded' 'partially_exposed' 'fully_exposed',
	122  'more_than_6' '1-5_(rarely)_6',
	123  'multinucleate' 'binucleate',
	124  'large,_completely_cellular' 'large,_apical_part_with_egg_free-nuclear' 'eight-nucleate',
	125  'diploid_zygotes' 'diploid_zygote_plus_triploid_endosperm',
	126  'horizontal' 'vertical' 'free-nuclear_phase',
	127  'exoscopic' 'endoscopic' 'prone',
	128  'absent' 'present',
	129  'large,_tapering' 'large,_bulbous' 'small,_bulbous' 'absent',