Bio-Phylo
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$tree->generize(
'-delim' => '_',
'-monotypic' => 1,
'-polypara' => 1,
);
$tree->get_logger->VERBOSE( '-level' => ERROR );
my $rep = $tree->replicate( '-genera' => 1 )->first;
ok( $rep );
ok( $tree->calc_number_of_terminals == $rep->calc_number_of_terminals );
# check for duplicate terminal labels in replicated tree
my %cnt, my %dup;
for ( map {$_->get_name} @{$rep->get_terminals} ) {
$dup{$_}++ if $cnt{$_}++;
}
ok ( ! scalar(keys%dup) );
};
__DATA__
#NEXUS
BEGIN TAXA;
[! Taxa block written by Bio::Phylo::Taxa 0.58 on Tue Aug 11 19:06:39 2015 ]
DIMENSIONS NTAX=100;
TAXLABELS
Allenopithecus_nigroviridis
Allocebus_trichotis
Alouatta_caraya
Alouatta_palliata
Aotus_azarai_infulatus
Aotus_trivirgatus
Arctocebus_calabarensis
Ateles_belzebuth_chamek
Ateles_fusciceps
Avahi_laniger
Brachyteles_arachnoides
Cacajao_calvus
Cacajao_melanocephalus
Callicebus_moloch
Callicebus_personatus
Callimico_goeldii
Callithrix_humeralifera
Callithrix_pygmaea
Cebus_albifrons
Cebus_apella
Cercocebus_galeritus
Cercocebus_torquatus
Cercopithecus_lhoesti
Cercopithecus_mona
Cheirogaleus_major
Cheirogaleus_medius
Chiropotes_albinasus
Chiropotes_satanas
Chlorocebus_aethiops
Colobus_angolensis
Colobus_guereza
Daubentonia_madagascariensis
Erythrocebus_patas
Eulemur_coronatus
Eulemur_rubriventer
Euoticus_elegantulus
Galago_alleni
Galago_senegalensis
Galagoides_demidoff
Galagoides_zanzibaricus
Gorilla_gorilla
Hapalemur_aureus
Hapalemur_simus
Homo_sapiens
Hoolock_hoolock
Hylobates_agilis
Hylobates_lar
Lagothrix_lagotricha
Lemur_catta
Leontopithecus_chrysopygus
Leontopithecus_rosalia
Lepilemur_mustelinus
Lepilemur_ruficaudatus
Lophocebus_albigena
Loris_tardigradus
Macaca_ochreata
Macaca_sylvanus
Mandrillus_leucophaeus
Mandrillus_sphinx
Microcebus_murinus
Microcebus_rufus
Miopithecus_talapoin
Mirza_coquereli
Nasalis_larvatus
Nomascus_concolor
Nomascus_gabriellae
Nycticebus_coucang
Nycticebus_pygmaeus
Otolemur_crassicaudatus
Otolemur_garnettii
Pan_paniscus
Pan_troglodytes
Papio_hamadryas
Perodicticus_potto
Phaner_furcifer
Piliocolobus_badius
Pithecia_irrorata
Pithecia_pithecia
Pongo_pygmaeus
Presbytis_comata
Presbytis_melalophos
Procolobus_verus
Propithecus_diadema
Propithecus_tattersalli
Pygathrix_nemaeus
Rhinopithecus_bieti
Rhinopithecus_roxellana
Saguinus_fuscicollis
Saguinus_imperator
Saimiri_sciureus
Saimiri_ustus
Semnopithecus_entellus
Simias_concolor
Symphalangus_syndactylus
Tarsius_syrichta
Tarsius_tarsier
Theropithecus_gelada
Trachypithecus_auratus
Trachypithecus_francoisi
Varecia_variegata
;
END;
BEGIN TREES;
[! Trees block written by Bio::Phylo::Forest 0.58 on Tue Aug 11 19:06:39 2015 ]
TRANSLATE
1 Daubentonia_madagascariensis,
2 Tarsius_tarsier,
3 Tarsius_syrichta,
4 Galagoides_zanzibaricus,
5 Phaner_furcifer,
6 Arctocebus_calabarensis,
7 Perodicticus_potto,
8 Loris_tardigradus,
9 Galagoides_demidoff,
10 Lepilemur_mustelinus,
11 Lepilemur_ruficaudatus,
12 Avahi_laniger,
13 Nycticebus_pygmaeus,
14 Nycticebus_coucang,
15 Chiropotes_albinasus,
16 Callicebus_personatus,
17 Callicebus_moloch,
18 Hoolock_hoolock,
19 Pongo_pygmaeus,
20 Propithecus_tattersalli,
21 Propithecus_diadema,
22 Galago_senegalensis,
23 Euoticus_elegantulus,
24 Galago_alleni,
25 Alouatta_caraya,
26 Alouatta_palliata,
27 Gorilla_gorilla,
28 Miopithecus_talapoin,
29 Cheirogaleus_major,
30 Cheirogaleus_medius,
31 Allocebus_trichotis,
32 Eulemur_coronatus,
33 Eulemur_rubriventer,
34 Otolemur_crassicaudatus,
35 Otolemur_garnettii,
36 Aotus_azarai_infulatus,
37 Aotus_trivirgatus,
38 Saimiri_ustus,
39 Saimiri_sciureus,
40 Cebus_albifrons,
41 Cebus_apella,
42 Brachyteles_arachnoides,
43 Lagothrix_lagotricha,
44 Ateles_belzebuth_chamek,
45 Ateles_fusciceps,
46 Cacajao_melanocephalus,
47 Pithecia_irrorata,
48 Pithecia_pithecia,
49 Nomascus_gabriellae,
50 Nomascus_concolor,
51 Symphalangus_syndactylus,
52 Homo_sapiens,
53 Colobus_angolensis,
54 Colobus_guereza,
55 Procolobus_verus,
56 Piliocolobus_badius,
57 Presbytis_comata,
58 Presbytis_melalophos,
59 Macaca_sylvanus,
60 Macaca_ochreata,
61 Allenopithecus_nigroviridis,
62 Mirza_coquereli,
63 Varecia_variegata,
64 Hapalemur_simus,
65 Hapalemur_aureus,
66 Lemur_catta,
67 Saguinus_fuscicollis,
68 Saguinus_imperator,
69 Cacajao_calvus,
70 Chiropotes_satanas,
71 Hylobates_lar,
72 Hylobates_agilis,
73 Pan_paniscus,
74 Pan_troglodytes,
75 Semnopithecus_entellus,
76 Pygathrix_nemaeus,
77 Cercocebus_galeritus,
78 Theropithecus_gelada,
79 Cercopithecus_mona,
80 Microcebus_murinus,
81 Microcebus_rufus,
82 Callimico_goeldii,
83 Leontopithecus_chrysopygus,
84 Leontopithecus_rosalia,
85 Trachypithecus_auratus,
86 Trachypithecus_francoisi,
87 Cercocebus_torquatus,
88 Papio_hamadryas,
89 Lophocebus_albigena,
90 Erythrocebus_patas,
91 Callithrix_pygmaea,
92 Callithrix_humeralifera,
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