[Phylobase-commits] r849 - pkg/inst/nexusfiles
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 13 17:12:22 CET 2014
Author: francois
Date: 2014-02-13 17:12:22 +0100 (Thu, 13 Feb 2014)
New Revision: 849
Added:
pkg/inst/nexusfiles/NastyLabels.nex
pkg/inst/nexusfiles/NastyLabels2.nex
pkg/inst/nexusfiles/minNex.nex
pkg/inst/nexusfiles/minSeq.nex
pkg/inst/nexusfiles/shorebird_underscore.nex
pkg/inst/nexusfiles/treeWithSpecialCharacters.nex
Log:
updating nexus files, not sure if needed
Added: pkg/inst/nexusfiles/NastyLabels.nex
===================================================================
--- pkg/inst/nexusfiles/NastyLabels.nex (rev 0)
+++ pkg/inst/nexusfiles/NastyLabels.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,56 @@
+#NEXUS
+[Data from Gavin Thomas]
+BEGIN TAXA;
+ DIMENSIONS NTAX = 11;
+ TAXLABELS
+ subterraneus
+ Mus_musculus
+ H._sapiens
+ 'H. sapiens #429'
+ 'Fred''s new sp.'
+ 'rusticus (1)'
+ '"shoal bass"'
+ AMNION
+ _23
+ x21.02
+ myType
+ ;
+end;
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD SYMBOLS="0 1";
+ CHARSTATELABELS
+ 1 aCharacter / on off;
+ MATRIX
+ subterraneus 0
+ Mus_musculus 1
+ H._sapiens 0
+ 'H. sapiens #429' 1
+ 'Fred''s new sp.' 0
+ 'rusticus (1)' 1
+ '"shoal bass"' 0
+ AMNION 1
+ _23 0
+ x21.02 1
+ myType 0
+ ;
+END;
+
+BEGIN TREES;
+ TRANSLATE
+ 1 subterraneus,
+ 2 Mus_musculus,
+ 3 H._sapiens,
+ 4 'H. sapiens #429',
+ 5 'Fred''s new sp.',
+ 6 'rusticus (1)',
+ 7 '"shoal bass"',
+ 8 AMNION,
+ 9 _23,
+ 10 x21.02,
+ 11 myType
+ ;
+ TREE * COMB = (1,(2,(3,(4,(5,(6,(7,(8,(9,(10,11))))))))));
+end;
+
Added: pkg/inst/nexusfiles/NastyLabels2.nex
===================================================================
--- pkg/inst/nexusfiles/NastyLabels2.nex (rev 0)
+++ pkg/inst/nexusfiles/NastyLabels2.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,52 @@
+#NEXUS
+
+
+begin data;
+ dimensions ntax=17 nchar=432;
+ format datatype=dna missing=?;
+ matrix
+ 'h uman' ctgactcctgaggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctgctggtggtctacccttggacccagaggttctttgagtcctttggggatctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcatggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggacaacctcaagggcacctttgccacactgagtgagctgcactgtgacaagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtctgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcaggctgcctatcagaaagtggtggctggtgtggctaatgccctggcccacaagtatcac
+ t_arsier ctgactgctgaagagaaggccgccgtcactgccctgtggggcaaggtagacgtggaagatgttggtggtgaggccctgggcaggctgctggtcgtctacccatggacccagaggttctttgactcctttggggacctgtccactcctgccgctgttatgagcaatgctaaggtcaaggcccatggcaaaaaggtgctgaacgcctttagtgacggcatggctcatctggacaacctcaagggcacctttgctaagctgagtgagctgcactgtgacaaattgcacgtggatcctgagaatttcaggctcttgggcaatgtgctggtgtgtgtgctggcccaccactttggcaaagaattcaccccgcaggttcaggctgcctatcagaaggtggtggctggtgtggctactgccttggctcacaagtaccac
+ 'b_ushbaby' ctgactcctgatgagaagaatgccgtttgtgccctgtggggcaaggtgaatgtggaagaagttggtggtgaggccctgggcaggctgctggttgtctacccatggacccagaggttctttgactcctttggggacctgtcctctccttctgctgttatgggcaaccctaaagtgaaggcccacggcaagaaggtgctgagtgcctttagcgagggcctgaatcacctggacaacctcaagggcacctttgctaagctgagtgagctgcattgtgacaagctgcacgtggaccctgagaacttcaggctcctgggcaacgtgctggtggttgtcctggctcaccactttggcaaggatttcaccccacaggtgcaggctgcctatcagaaggtggtggctggtgtggctactgccctggctcacaaataccac
+ 'ha re' ctgtccggtgaggagaagtctgcggtcactgccctgtggggcaaggtgaatgtggaagaagttggtggtgagaccctgggcaggctgctggttgtctacccatggacccagaggttcttcgagtcctttggggacctgtccactgcttctgctgttatgggcaaccctaaggtgaaggctcatggcaagaaggtgctggctgccttcagtgagggtctgagtcacctggacaacctcaaaggcaccttcgctaagctgagtgaactgcattgtgacaagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggttattgtgctgtctcatcactttggcaaagaattcactcctcaggtgcaggctgcctatcagaaggtggtggctggtgtggccaatgccctggctcacaaataccac
+ 'ra\bbit' ctgtccagtgaggagaagtctgcggtcactgccctgtggggcaaggtgaatgtggaagaagttggtggtgaggccctgggcaggctgctggttgtctacccatggacccagaggttcttcgagtcctttggggacctgtcctctgcaaatgctgttatgaacaatcctaaggtgaaggctcatggcaagaaggtgctggctgccttcagtgagggtctgagtcacctggacaacctcaaaggcacctttgctaagctgagtgaactgcactgtgacaagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggttattgtgctgtctcatcattttggcaaagaattcactcctcaggtgcaggctgcctatcagaaggtggtggctggtgtggccaatgccctggctcacaaataccac
+ 'co''w' ctgactgctgaggagaaggctgccgtcaccgccttttggggcaaggtgaaagtggatgaagttggtggtgaggccctgggcaggctgctggttgtctacccctggactcagaggttctttgagtcctttggggacttgtccactgctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagattcctttagtaatggcatgaagcatctcgatgacctcaagggcacctttgctgcgctgagtgagctgcactgtgataagctgcatgtggatcctgagaacttcaagctcctgggcaacgtgctagtggttgtgctggctcgcaattttggcaaggaattcaccccggtgctgcaggctgactttcagaaggtggtggctggtgtggccaatgccctggcccacagatatcat
+ 'sh"eep' ctgactgctgaggagaaggctgccgtcaccggcttctggggcaaggtgaaagtggatgaagttggtgctgaggccctgggcaggctgctggttgtctacccctggactcagaggttctttgagcactttggggacttgtccaatgctgatgctgttatgaacaaccctaaggtgaaggcccatggcaagaaggtgctagactcctttagtaacggcatgaagcatctcgatgacctcaagggcacctttgctcagctgagtgagctgcactgtgataagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtggttgtgctggctcgccaccatggcaatgaattcaccccggtgctgcaggctgactttcagaaggtggtggctggtgttgccaatgccctggcccacaaatatcac
+ pig ctgtctgctgaggagaaggaggccgtcctcggcctgtggggcaaagtgaatgtggacgaagttggtggtgaggccctgggcaggctgctggttgtctacccctggactcagaggttcttcgagtcctttggggacctgtccaatgccgatgccgtcatgggcaatcccaaggtgaaggcccacggcaagaaggtgctccagtccttcagtgacggcctgaaacatctcgacaacctcaagggcacctttgctaagctgagcgagctgcactgtgaccagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgatagtggttgttctggctcgccgccttggccatgacttcaacccgaatgtgcaggctgcttttcagaaggtggtggctggtgttgctaatgccctggcccacaagtaccac
+ elephseal ttgacggcggaggagaagtctgccgtcacctccctgtggggcaaagtgaaggtggatgaagttggtggtgaagccctgggcaggctgctggttgtctacccctggactcagaggttctttgactcctttggggacctgtcctctcctaatgctattatgagcaaccccaaggtcaaggcccatggcaagaaggtgctgaattcctttagtgatggcctgaagaatctggacaacctcaagggcacctttgctaagctcagtgagctgcactgtgaccagctgcatgtggatcccgagaacttcaagctcctgggcaatgtgctggtgtgtgtgctggcccgccactttggcaaggaattcaccccacagatgcagggtgcctttcagaaggtggtagctggtgtggccaatgccctcgcccacaaatatcac
+ rat ctaactgatgctgagaaggctgctgttaatgccctgtggggaaaggtgaaccctgatgatgttggtggcgaggccctgggcaggctgctggttgtctacccttggacccagaggtactttgatagctttggggacctgtcctctgcctctgctatcatgggtaaccctaaggtgaaggcccatggcaagaaggtgataaacgccttcaatgatggcctgaaacacttggacaacctcaagggcacctttgctcatctgagtgaactccactgtgacaagctgcatgtggatcctgagaacttcaggctcctgggcaatatgattgtgattgtgttgggccaccacctgggcaaggaattcaccccctgtgcacaggctgccttccagaaggtggtggctggagtggccagtgccctggctcacaagtaccac
+ mouse ctgactgatgctgagaagtctgctgtctcttgcctgtgggcaaaggtgaaccccgatgaagttggtggtgaggccctgggcaggctgctggttgtctacccttggacccagcggtactttgatagctttggagacctatcctctgcctctgctatcatgggtaatcccaaggtgaaggcccatggcaaaaaggtgataactgcctttaacgagggcctgaaaaacctggacaacctcaagggcacctttgccagcctcagtgagctccactgtgacaagctgcatgtggatcctgagaacttcaggctcctaggcaatgcgatcgtgattgtgctgggccaccacctgggcaaggatttcacccctgctgcacaggctgccttccagaaggtggtggctggagtggccactgccctggctcacaagtaccac
+ hamster ctgactgatgctgagaaggcccttgtcactggcctgtggggaaaggtgaacgccgatgcagttggcgctgaggccctgggcaggttgctggttgtctacccttggacccagaggttctttgaacactttggagacctgtctctgccagttgctgtcatgaataacccccaggtgaaggcccatggcaagaaggtgatccactccttcgctgatggcctgaaacacctggacaacctgaagggcgccttttccagcctgagtgagctccactgtgacaagctgcacgtggatcctgagaacttcaagctcctgggcaatatgatcatcattgtgctgatccacgacctgggcaaggacttcactcccagtgcacagtctgcctttcataaggtggtggctggtgtggccaatgccctggctcacaagtaccac
+ marsupial ttgacttctgaggagaagaactgcatcactaccatctggtctaaggtgcaggttgaccagactggtggtgaggcccttggcaggatgctcgttgtctacccctggaccaccaggttttttgggagctttggtgatctgtcctctcctggcgctgtcatgtcaaattctaaggttcaagcccatggtgctaaggtgttgacctccttcggtgaagcagtcaagcatttggacaacctgaagggtacttatgccaagttgagtgagctccactgtgacaagctgcatgtggaccctgagaacttcaagatgctggggaatatcattgtgatctgcctggctgagcactttggcaaggattttactcctgaatgtcaggttgcttggcagaagctcgtggctggagttgcccatgccctggcccacaagtaccac
+ duck tggacagccgaggagaagcagctcatcaccggcctctggggcaaggtcaatgtggccgactgtggagctgaggccctggccaggctgctgatcgtctacccctggacccagaggttcttcgcctccttcgggaacctgtccagccccactgccatccttggcaaccccatggtccgtgcccatggcaagaaagtgctcacctccttcggagatgctgtgaagaacctggacaacatcaagaacaccttcgcccagctgtccgagctgcactgcgacaagctgcacgtggaccctgagaacttcaggctcctgggtgacatcctcatcatcgtcctggccgcccacttcaccaaggatttcactcctgactgccaggccgcctggcagaagctggtccgcgtggtggcccacgctctggcccgcaagtaccac
+ chicken tggactgctgaggagaagcagctcatcaccggcctctggggcaaggtcaatgtggccgaatgtggggccgaagccctggccaggctgctgatcgtctacccctggacccagaggttctttgcgtcctttgggaacctctccagccccactgccatccttggcaaccccatggtccgcgcccacggcaagaaagtgctcacctcctttggggatgctgtgaagaacctggacaacatcaagaacaccttctcccaactgtccgaactgcattgtgacaagctgcatgtggaccccgagaacttcaggctcctgggtgacatcctcatcattgtcctggccgcccacttcagcaaggacttcactcctgaatgccaggctgcctggcagaagctggtccgcgtggtggcccatgccctggctcgcaagtaccac
+ xenlaev tggacagctgaagagaaggccgccatcacttctgtatggcagaaggtcaatgtagaacatgatggccatgatgccctgggcaggctgctgattgtgtacccctggacccagagatacttcagtaactttggaaacctctccaattcagctgctgttgctggaaatgccaaggttcaagcccatggcaagaaggttctttcagctgttggcaatgccattagccatattgacagtgtgaagtcctctctccaacaactcagtaagatccatgccactgaactgtttgtggaccctgagaactttaagcgttttggtggagttctggtcattgtcttgggtgccaaactgggaactgccttcactcctaaagttcaggctgcttgggagaaattcattgcagttttggttgatggtcttagccagggctataac
+ xentrop tggacagctgaagaaaaagcaaccattgcttctgtgtgggggaaagtcgacattgaacaggatggccatgatgcattatccaggctgctggttgtttatccctggactcagaggtacttcagcagttttggaaacctctccaatgtctccgctgtctctggaaatgtcaaggttaaagcccatggaaataaagtcctgtcagctgttggcagtgcaatccagcatctggatgatgtgaagagccaccttaaaggtcttagcaagagccatgctgaggatcttcatgtggatcccgaaaacttcaagcgccttgcggatgttctggtgatcgttctggctgccaaacttggatctgccttcactccccaagtccaagctgtctgggagaagctcaatgcaactctggtggctgctcttagccatggctacttc
+ ;
+end;
+
+
+begin mrbayes;
+ [The following block illustrates how to set up two data partitions
+ and use different models for the different partitions.]
+ charset non_coding = 1-90 358-432;
+ charset coding = 91-357;
+ partition region = 2:non_coding,coding;
+ set partition = region;
+
+ [The following lines set a codon model for the second data partition (coding) and
+ allows the non_coding and coding partitions to have different overall rates.]
+ lset applyto=(2) nucmodel=codon;
+ prset ratepr=variable;
+
+ [Codon models are computationally complex so the following lines set the parameters
+ of the MCMC such that only 1 chain is run for 100 generations and results are printed
+ to screen and to file every tenth generation. To start this chain, you need to type
+ 'mcmc' after executing this block. You need to run the chain longer to get adequate
+ convergence.]
+ mcmcp ngen=100 nchains=1 printfreq=10 samplefreq=10;
+end;
+
+
+
+
Added: pkg/inst/nexusfiles/minNex.nex
===================================================================
--- pkg/inst/nexusfiles/minNex.nex (rev 0)
+++ pkg/inst/nexusfiles/minNex.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,56 @@
+#NEXUS
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=4;
+ TAXLABELS
+ spA spB spC spD
+ ;
+
+END;
+
+BEGIN TREES;
+ TRANSLATE
+ 1 spA,
+ 2 spB,
+ 3 spC,
+ 4 spD;
+ TREE testTree = (1,(2,(3,4)));
+END;
+
+BEGIN CHARACTERS;
+ TITLE 'TestContinuous';
+ DIMENSIONS NCHAR=3;
+ FORMAT DATATYPE = CONTINUOUS;
+ CHARSTATELABELS
+ 1 char1,
+ 2 char2,
+ 3 char3;
+ MATRIX
+ spB 0.21 0.22 0.23
+ spA 0.11 0.12 0.13
+ spD 0.41 0.42 0.43
+ spC 0.31 0.32 0.33
+ ;
+END;
+
+BEGIN CHARACTERS;
+ TITLE 'TestStd';
+ DIMENSIONS NCHAR=3;
+ FORMAT DATATYPE = STANDARD
+ MISSING = ?
+ SYMBOLS = "0 1 2";
+ CHARSTATELABELS
+ 1 char1 / state11 state12 state13,
+ 2 char2 / state21 state22 state23,
+ 3 char3 / state31 state32 state33;
+ MATRIX
+ spA 1 (0 1) ?
+ spB 2 (1 2) 0
+ spC 0 (0 1 2) 1
+ spD 1 2 0
+ ;
+END;
+
+[BEGIN ASSUMPTIONS;
+ EXSET * UNTITLED = 3;
+END;]
Added: pkg/inst/nexusfiles/minSeq.nex
===================================================================
--- pkg/inst/nexusfiles/minSeq.nex (rev 0)
+++ pkg/inst/nexusfiles/minSeq.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,12 @@
+#NEXUS
+
+
+begin data;
+ dimensions ntax=3 nchar=4;
+ format datatype=dna missing=?;
+ matrix
+ seq1 atcg
+ seq2 tcga
+ seq3 cgat
+ ;
+end;
Added: pkg/inst/nexusfiles/shorebird_underscore.nex
===================================================================
--- pkg/inst/nexusfiles/shorebird_underscore.nex (rev 0)
+++ pkg/inst/nexusfiles/shorebird_underscore.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,321 @@
+#NEXUS
+[Data from Gavin Thomas]
+BEGIN TAXA;
+ DIMENSIONS NTAX = 71;
+ TAXLABELS
+ Catoptrophorus_semipalmatus
+ Tringa_ochropus
+ Tringa_stagnatilis
+ Tringa_flavipes
+ Tringa_nebularia
+ Tringa_totanus
+ Tringa_erythropus
+ Tringa_melanoleuca
+ Tringa_glareola
+ Steganopus_tricolor
+ Phalaropus_lobatus
+ Phalaropus_fulicaria
+ Micropalama_himantopus
+ Eurynorhynchus_pygmeus
+ Aphriza_virgata
+ Calidris_canutus
+ Calidris_tenuirostris
+ Calidris_temminckii
+ Calidris_maritima
+ Calidris_ptilocnemis
+ Calidris_mauri
+ Calidris_alba
+ Calidris_alpina
+ Calidris_bairdii
+ Calidris_minutilla
+ Calidris_pusilla
+ Calidris_minuta
+ Calidris_ruficollis
+ Calidris_subminuta
+ Arenaria_interpres
+ Arenaria_melanocephala
+ Tringa_hypoleucos
+ Tringa_macularia
+ Limnodromus_griseus
+ Gallinago_gallinago
+ Coenocorypha_aucklandica
+ Coenocorypha_pusilla
+ Limosa_fedoa
+ Limosa_haemastica
+ Limosa_limosa
+ Limosa_lapponica
+ Bartramia_longicauda
+ Numenius_tahitiensis
+ Numenius_phaeopus
+ Numenius_arquata
+ Numenius_americanus
+ Rostratula_benghalensis
+ Jacana_spinosa
+ Jacana_jacana
+ Metopidius_indicus
+ Actophilornis_africanus
+ Pedionomus_torquatus
+ Pluvialis_apricaria
+ Pluvialis_dominica
+ Eudromias_morinellus
+ Charadrius_montanus
+ Charadrius_vociferus
+ Charadrius_wilsonia
+ Charadrius_dubius
+ Charadrius_hiaticula
+ Charadrius_melodus
+ Vanellus_vanellus
+ Vanellus_lugubris
+ Vanellus_armatus
+ Recurvirostra_avosetta
+ Haematopus_longirostris
+ Haematopus_fuliginosus
+ Haematopus_moquini
+ Haematopus_ostralegus
+ Haematopus_unicolor
+ Haematopus_finschi
+ ;
+END;
+
+BEGIN CHARACTERS;
+ TITLE MassClutchSize;
+ DIMENSIONS NCHAR=4;
+ FORMAT DATATYPE = CONTINUOUS;
+ CHARSTATELABELS
+ 1 malemass,
+ 2 femalemass,
+ 3 eggmass,
+ 4 clutchsize;
+ MATRIX
+ Actophilornis_africanus 143.2 260.7 8.6 4.00
+ Aphriza_virgata 186.3 216.3 22.4 4.00
+ Arenaria_interpres 108.0 113.0 17.9 3.50
+ Arenaria_melanocephala 113.6 124.2 17.3 4.00
+ Bartramia_longicauda 151.0 164.0 23.5 3.99
+ Calidris_alba 52.8 55.4 11.2 3.90
+ Calidris_alpina 41.0 45.1 10.7 3.90
+ Calidris_bairdii 39.3 39.7 9.6 4.00
+ Calidris_canutus 126.0 148.0 19.3 3.70
+ Calidris_maritima 67.6 76.3 13.3 3.90
+ Calidris_mauri 28.0 31.0 7.5 3.90
+ Calidris_minuta 24.0 27.1 6.3 3.80
+ Calidris_minutilla 20.3 22.2 6.4 3.90
+ Calidris_ptilocnemis 76.3 83.0 14.2 4.00
+ Calidris_pusilla 25.0 27.0 6.9 4.00
+ Calidris_ruficollis 25.7 26.6 8.3 4.00
+ Calidris_subminuta 29.0 32.0 7.5 4.00
+ Calidris_temminckii 24.3 27.8 5.8 4.00
+ Calidris_tenuirostris 156.0 174.0 22.0 4.00
+ Catoptrophorus_semipalmatus 273.0 301.4 39.5 4.00
+ Charadrius_dubius 38.3 39.2 7.7 3.90
+ Charadrius_hiaticula 63.5 64.7 10.9 3.80
+ Charadrius_melodus 54.9 55.6 9.4 3.30
+ Charadrius_montanus 102.0 114.0 16.5 3.00
+ Charadrius_vociferus 92.1 101.0 14.5 4.00
+ Charadrius_wilsonia 59.0 63.0 12.4 3.00
+ Coenocorypha_aucklandica 101.2 116.1 23.7 2.00
+ Coenocorypha_pusilla 75.9 85.4 16.1 2.10
+ Eudromias_morinellus 100.0 117.0 17.0 2.90
+ Eurynorhynchus_pygmeus 31.0 34.6 8.0 4.00
+ Gallinago_gallinago 111.0 128.0 16.5 3.90
+ Haematopus_finschi 517.0 554.0 44.2 2.33
+ Haematopus_fuliginosus 740.3 778.5 69.5 2.00
+ Haematopus_longirostris 602.3 626.3 49.0 2.50
+ Haematopus_moquini 668.0 730.0 55.8 1.70
+ Haematopus_ostralegus 500.0 536.0 46.7 2.80
+ Haematopus_unicolor 717.0 734.0 48.2 2.40
+ Jacana_jacana 108.3 142.8 9.7 3.50
+ Jacana_spinosa 86.9 145.4 8.3 4.00
+ Limnodromus_griseus 111.0 116.0 17.5 4.10
+ Limosa_fedoa 320.0 421.0 44.5 4.10
+ Limosa_haemastica 222.0 289.0 37.5 4.00
+ Limosa_lapponica 313.0 354.0 37.0 3.72
+ Limosa_limosa 264.0 315.0 39.0 3.90
+ Metopidius_indicus 176.2 282.4 11.9 4.00
+ Micropalama_himantopus 55.8 60.4 11.2 3.90
+ Numenius_americanus 640.1 758.6 73.0 4.00
+ Numenius_arquata 662.0 788.0 76.0 3.90
+ Numenius_phaeopus 368.0 398.0 50.0 3.90
+ Numenius_tahitiensis 378.0 489.0 54.8 4.00
+ Pedionomus_torquatus 54.0 72.4 10.0 3.60
+ Phalaropus_fulicaria 50.8 61.0 7.5 3.80
+ Phalaropus_lobatus 32.4 37.4 6.3 4.00
+ Pluvialis_apricaria 175.0 176.0 32.8 3.90
+ Pluvialis_dominica 145.0 146.0 26.0 4.00
+ Recurvirostra_avosetta 258.0 288.0 31.7 3.90
+ Rostratula_benghalensis 146.0 159.0 12.4 4.00
+ Steganopus_tricolor 50.2 68.1 9.4 4.00
+ Tringa_erythropus 142.0 161.0 24.5 4.00
+ Tringa_flavipes 80.0 83.7 17.4 4.00
+ Tringa_glareola 62.0 73.0 13.5 4.00
+ Tringa_hypoleucos 45.5 50.0 12.5 3.90
+ Tringa_macularia 36.9 48.0 9.0 4.00
+ Tringa_melanoleuca 164.0 176.0 27.9 3.70
+ Tringa_nebularia 172.0 175.0 30.5 3.90
+ Tringa_ochropus 75.0 85.0 15.5 3.90
+ Tringa_stagnatilis 67.1 76.0 14.0 4.00
+ Tringa_totanus 123.0 135.0 22.3 4.00
+ Vanellus_armatus 162.0 167.0 16.5 3.10
+ Vanellus_lugubris 109.5 113.0 13.7 3.00
+ Vanellus_vanellus 211.0 226.0 25.5 3.90
+ ;
+END;
+
+BEGIN CHARACTERS;
+ TITLE MatingSystem;
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD SYMBOLS="0 1 2";
+ CHARSTATELABELS
+ 1 matingSystem / Monogamous Polygynous Polyandrous;
+ MATRIX
+ Actophilornis_africanus 2
+ Aphriza_virgata 0
+ Arenaria_interpres 0
+ Arenaria_melanocephala 0
+ Bartramia_longicauda 0
+ Calidris_alba 2
+ Calidris_alpina 0
+ Calidris_bairdii 0
+ Calidris_canutus 0
+ Calidris_maritima 0
+ Calidris_mauri 0
+ Calidris_minuta 2
+ Calidris_minutilla 0
+ Calidris_ptilocnemis 0
+ Calidris_pusilla 0
+ Calidris_ruficollis 0
+ Calidris_subminuta 0
+ Calidris_temminckii 2
+ Calidris_tenuirostris 0
+ Catoptrophorus_semipalmatus 0
+ Charadrius_dubius 0
+ Charadrius_hiaticula 0
+ Charadrius_melodus 0
+ Charadrius_montanus 2
+ Charadrius_vociferus 0
+ Charadrius_wilsonia 0
+ Coenocorypha_aucklandica 1
+ Coenocorypha_pusilla 0
+ Eudromias_morinellus 2
+ Eurynorhynchus_pygmeus 0
+ Gallinago_gallinago 0
+ Haematopus_finschi 0
+ Haematopus_fuliginosus 0
+ Haematopus_longirostris 0
+ Haematopus_moquini 0
+ Haematopus_ostralegus 0
+ Haematopus_unicolor 0
+ Jacana_jacana 2
+ Jacana_spinosa 2
+ Limnodromus_griseus 0
+ Limosa_fedoa 0
+ Limosa_haemastica 0
+ Limosa_lapponica 0
+ Limosa_limosa 0
+ Metopidius_indicus 2
+ Micropalama_himantopus 0
+ Numenius_americanus 0
+ Numenius_arquata 0
+ Numenius_phaeopus 0
+ Numenius_tahitiensis 0
+ Pedionomus_torquatus 2
+ Phalaropus_fulicaria 2
+ Phalaropus_lobatus 2
+ Pluvialis_apricaria 0
+ Pluvialis_dominica 0
+ Recurvirostra_avosetta 0
+ Rostratula_benghalensis 2
+ Steganopus_tricolor 2
+ Tringa_erythropus 0
+ Tringa_flavipes 0
+ Tringa_glareola 0
+ Tringa_hypoleucos 0
+ Tringa_macularia 2
+ Tringa_melanoleuca 0
+ Tringa_nebularia 0
+ Tringa_ochropus 0
+ Tringa_stagnatilis 0
+ Tringa_totanus 0
+ Vanellus_armatus 0
+ Vanellus_lugubris 0
+ Vanellus_vanellus 1
+ ;
+END;
+
+
+BEGIN TREES;
+ TRANSLATE
+ 1 Catoptrophorus_semipalmatus,
+ 2 Tringa_ochropus,
+ 3 Tringa_stagnatilis,
+ 4 Tringa_flavipes,
+ 5 Tringa_nebularia,
+ 6 Tringa_totanus,
+ 7 Tringa_erythropus,
+ 8 Tringa_melanoleuca,
+ 9 Tringa_glareola,
+ 10 Steganopus_tricolor,
+ 11 Phalaropus_lobatus,
+ 12 Phalaropus_fulicaria,
+ 13 Micropalama_himantopus,
+ 14 Eurynorhynchus_pygmeus,
+ 15 Aphriza_virgata,
+ 16 Calidris_canutus,
+ 17 Calidris_tenuirostris,
+ 18 Calidris_temminckii,
+ 19 Calidris_maritima,
+ 20 Calidris_ptilocnemis,
+ 21 Calidris_mauri,
+ 22 Calidris_alba,
+ 23 Calidris_alpina,
+ 24 Calidris_bairdii,
+ 25 Calidris_minutilla,
+ 26 Calidris_pusilla,
+ 27 Calidris_minuta,
+ 28 Calidris_ruficollis,
+ 29 Calidris_subminuta,
+ 30 Arenaria_interpres,
+ 31 Arenaria_melanocephala,
+ 32 Tringa_hypoleucos,
+ 33 Tringa_macularia,
+ 34 Limnodromus_griseus,
+ 35 Gallinago_gallinago,
+ 36 Coenocorypha_aucklandica,
+ 37 Coenocorypha_pusilla,
+ 38 Limosa_fedoa,
+ 39 Limosa_haemastica,
+ 40 Limosa_limosa,
+ 41 Limosa_lapponica,
+ 42 Bartramia_longicauda,
+ 43 Numenius_tahitiensis,
+ 44 Numenius_phaeopus,
+ 45 Numenius_arquata,
+ 46 Numenius_americanus,
+ 47 Rostratula_benghalensis,
+ 48 Jacana_spinosa,
+ 49 Jacana_jacana,
+ 50 Metopidius_indicus,
+ 51 Actophilornis_africanus,
+ 52 Pedionomus_torquatus,
+ 53 Pluvialis_apricaria,
+ 54 Pluvialis_dominica,
+ 55 Eudromias_morinellus,
+ 56 Charadrius_montanus,
+ 57 Charadrius_vociferus,
+ 58 Charadrius_wilsonia,
+ 59 Charadrius_dubius,
+ 60 Charadrius_hiaticula,
+ 61 Charadrius_melodus,
+ 62 Vanellus_vanellus,
+ 63 Vanellus_lugubris,
+ 64 Vanellus_armatus,
+ 65 Recurvirostra_avosetta,
+ 66 Haematopus_longirostris,
+ 67 Haematopus_fuliginosus,
+ 68 Haematopus_moquini,
+ 69 Haematopus_ostralegus,
+ 70 Haematopus_unicolor,
+ 71 Haematopus_finschi
+ ;
+ TREE * UNTITLED = [&R] ((((((((1:19.701,(2:19.086,((3:13.762,4:13.762,5:13.762,6:13.762,(7:5.324,8:5.324):8.438):3.114,9:16.876):2.21):0.615):2.499,(10:3.42,(11:2.158,12:2.158):1.262):18.78):9.9,((13:17.413,14:17.413,(15:6.019,(16:3.798,17:3.798):2.221):11.394,(18:10.013,((19:2.588,20:2.588):6.989,(21:9.142,(22:8.707,((23:7.836,(24:7.4,(25:6.965,(26:3.483,27:3.483):3.482):0.435):0.436):0.435,(28:2.609,29:2.609):5.662):0.436):0.435):0.435):0.436):7.4):9.287,(30:5.68,31:5.68):21.02):5.4,(32:5.779,33:5.779):26.320999):2.3,(34:23.8,(35:22.8,(36:4.91,37:4.91):17.889999):1):10.6):2.6,(38:11.739,(39:9.303,(40:5.869,41:5.869):3.434):2.436):25.261):13.4,(42:20.299,(43:14.869,(44:10.15,(45:6.404,46:6.404):3.746):4.719):5.43):30.101):13.4,((47:43.3,((48:10.8,49:10.8):21.6,(50:19.845,51:19.845):12.555):10.9):8.8,52:52.099999):11.7):18.072,(((53:8.33,54:8.33):23.437001,((55:26.700001,(56:22.991999,((57:5.548,58:5.548):10.027,(59:12.882,(60:8.793,61:8.793):4.089):2.693):7.417):3.708):3,(62:22.961,63:22.960999,64:22.961):6.739):2.067):1.033,(65:19.1,(66:14.817,(67:12.849,(68:11.072,(69:4.283,70:4.283):6.789,71:11.072):1.777):1.968):4.283):13.7):49.071998);
+END;
Added: pkg/inst/nexusfiles/treeWithSpecialCharacters.nex
===================================================================
--- pkg/inst/nexusfiles/treeWithSpecialCharacters.nex (rev 0)
+++ pkg/inst/nexusfiles/treeWithSpecialCharacters.nex 2014-02-13 16:12:22 UTC (rev 849)
@@ -0,0 +1,35 @@
+#NEXUS
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=6;
+ TAXLABELS
+ Species_1 'Species 2' 'Species 3' 'Species/4' 'Species\5' 'Species"6'
+ ;
+END;
+
+BEGIN CHARACTERS;
+ TITLE TestCharacters;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 character1 / state1.1 'state 1.2', 2 character2 / state2.1 'state 2 2';
+ MATRIX
+ Species_1 01
+ 'Species 2' 10
+ 'Species 3' 11
+ 'Species/4' 00
+ 'Species\5' 01
+ 'Species"6' ?1
+ ;
+END;
+
+BEGIN TREES;
+ TRANSLATE
+ 1 Species_1,
+ 2 'Species 2',
+ 3 'Species 3',
+ 4 'Species/4',
+ 5 'Species\5',
+ 6 'Species"6';
+ TREE tree1 = ((((1,2),3),4),5);
+END;
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