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bcbi · Oct 5, 2021 · 8fd9354 · 8fd9354
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diff --git a/Trees and Matrices/gi_choPhyla.nex → Trees and Matrices/gi_phyla.nex b/Trees and Matrices/gi_choPhyla.nex → Trees and Matrices/gi_phyla.nex
diff --git a/Trees and Matrices/gi_choPhyla.tre → Trees and Matrices/gi_phyla.tre b/Trees and Matrices/gi_choPhyla.tre → Trees and Matrices/gi_phyla.tre
diff --git a/Trees and Matrices/gi_tangle.nex b/Trees and Matrices/gi_tangle.nex
@@ -0,0 +1,35 @@
+#NEXUS
+begin data;
+dimensions ntax=28 nchar=49;
+charlabels Synergistetes Evosea Nematoda Statovirus Blastocystis Peploviricota Verrucomicrobia Preplasmiviricota Ascomycota Iotatorquevirus Apicomplexa Elusimicrobia Negarnaviricota Tenericutes Fusobacteria Cyanobacteria Duplornaviricota Annelida Chytridiomycota Artverviricota Firmicutes Parabasalia Gyrovirus Mucoromycota Cressdnaviricota Zoopagomycota Lentisphaerae Anelloviridae Fornicata Basidiomycota Ciliophora Chlorophyta Cossaviricota Euryarchaeota Phixviricota Kitrinoviricota Spirochaetes Euglenozoa Fibrobacteres Uroviricota Thetatorquevirus Proteobacteria Chlamydiae Bacteroidetes Actinobacteria Streptophyta Pisuviricota Deferribacteres Microsporidia;
+matrix
+Gallus_gallus 1 0 1 0 0 0 0 1 0 0 1 0 1 1 0 0 1 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 1 1 0 1 1 0 0 1 0 1 0 1 1 0 1 0 0
+Felis_catus 0 0 1 0 1 0 0 1 0 0 1 0 1 1 1 0 1 0 0 0 1 1 1 0 0 0 0 0 1 1 0 0 1 0 1 0 0 0 0 0 0 1 0 1 1 0 1 0 1
+Macaca_mulatta 0 1 1 1 1 1 0 1 0 0 1 0 1 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 1 0 1 1 0 1 0 1
+Mastomys_natalensis 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Buffalo 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 1 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0
+Equus_caballus 0 0 1 0 0 0 0 0 0 0 1 1 0 1 0 0 1 0 1 0 1 0 0 1 0 0 0 0 1 0 1 0 0 1 0 0 1 0 1 1 0 1 1 1 1 0 1 0 1
+Eidolon_helvum 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1
+Rattus_rattus 0 0 1 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 1 0 0
+Rhinolophus_ferrumequinum 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+Anas_platyrhynchos 0 0 1 0 1 1 0 1 0 0 1 0 1 0 1 0 1 0 0 1 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 1 1 0 0 0 0 1 0 1 1 0 1 0 1
+Carollia_perspicillata 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+Mus_musculus 0 0 1 0 0 0 1 1 1 0 1 0 1 1 0 0 1 0 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 1 1 0 1 1 0
+Ovis_aries 1 0 1 0 1 0 0 0 1 0 1 0 0 1 0 1 0 0 1 0 1 1 0 0 0 0 0 0 1 0 1 0 0 1 0 0 1 0 0 0 0 1 0 1 1 1 1 0 1
+Bos_taurus 1 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 1 0 1 0 1 0 0 1 0 0 0 0 1 1 1 0 0 1 0 1 1 0 0 0 0 1 1 1 1 0 1 0 0
+Canis_familiaris 0 0 1 0 0 0 0 1 1 0 1 0 1 0 0 0 1 0 0 0 1 1 0 0 1 0 0 0 1 1 0 1 1 0 0 1 0 0 0 0 1 1 0 1 1 0 1 0 1
+Rousettus_egyptiacus 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0
+Cavia_porcellus 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+Meleagris_gallopavo 0 0 1 0 1 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0
+Gorilla_beringei 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
+Capra_aegagrus_hircus 1 1 1 0 1 0 0 0 0 0 1 0 1 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0 1 0 1 0 0 1 0 0 1 0 0 1 0 1 0 1
+Bubalus_bubalis 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 1 1 0 0 0 0 0 0 1 0 1 0 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0
+Pan_troglodytes 0 0 1 0 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 1 0 1 0 0 1 1 0 0 0 0 1 0 0 1 0 1 0 0
+Sus_scrofa 1 0 1 0 1 0 0 0 0 1 1 0 0 1 1 0 1 0 0 0 1 0 0 0 1 0 1 0 1 0 0 0 1 0 0 1 1 0 0 0 0 1 0 1 1 0 1 0 1
+Columba_livia 0 0 1 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 1 0 1
+Rattus_exulans 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+Vulpes_vulpes 0 0 1 0 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0
+Rattus_norvegicus 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 1 1 0 0 0 1 0 1 1 0 1 0 0
+Homo_sapiens 0 1 1 0 0 0 1 1 1 0 1 0 0 1 1 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 0 1 1 1 1 0 1
+;
+end;
diff --git a/Trees and Matrices/gi_choTangle.tre → Trees and Matrices/gi_tangle.tre b/Trees and Matrices/gi_choTangle.tre → Trees and Matrices/gi_tangle.tre
diff --git a/Trees and Matrices/oral_choPhyla.nex → Trees and Matrices/oral_phyla.nex b/Trees and Matrices/oral_choPhyla.nex → Trees and Matrices/oral_phyla.nex
diff --git a/Trees and Matrices/oral_choPhyla.tre → Trees and Matrices/oral_phyla.tre b/Trees and Matrices/oral_choPhyla.tre → Trees and Matrices/oral_phyla.tre
diff --git a/Trees and Matrices/oral_tangle.nex b/Trees and Matrices/oral_tangle.nex
@@ -0,0 +1,35 @@
+#NEXUS
+begin data;
+dimensions ntax=28 nchar=24;
+charlabels Synergistetes Negarnaviricota Basidiomycota Tenericutes Fusobacteria Nematoda Cyanobacteria Proteobacteria Chlamydiae Bacteroidetes Actinobacteria Duplornaviricota Peploviricota Artverviricota Cossaviricota Firmicutes Preplasmiviricota Kitrinoviricota Apicomplexa Parabasalia Pisuviricota Spirochaetes Cressdnaviricota Anelloviridae;
+matrix
+Sus_scrofa 0 1 0 0 1 0 0 1 0 1 0 0 1 0 1 1 0 1 0 0 1 0 1 0
+Gorilla_beringei 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0
+Cavia_porcellus 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0
+Rattus_rattus 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
+Rhinolophus_ferrumequinum 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0
+Anas_platyrhynchos 0 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
+Vulpes_vulpes 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Rousettus_egyptiacus 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
+Columba_livia 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Rattus_exulans 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Bos_taurus 0 1 0 1 0 0 0 1 0 0 1 1 0 0 1 1 0 1 1 0 1 0 0 0
+Rattus_norvegicus 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 0 0 1 0 1 1
+Canis_familiaris 1 1 0 1 1 0 0 1 0 1 1 0 0 0 1 1 0 0 0 0 0 1 0 0
+Gallus_gallus 0 1 0 0 0 0 0 1 1 1 1 0 1 0 0 0 1 0 0 0 1 0 0 0
+Carollia_perspicillata 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0
+Equus_caballus 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 1 0 1 0 0
+Felis_catus 0 0 0 0 0 0 0 1 0 1 1 0 0 1 1 1 0 0 0 1 0 0 0 0
+Homo_sapiens 0 1 0 0 1 0 0 1 0 1 1 0 0 0 0 1 1 1 0 0 1 1 0 0
+Eidolon_helvum 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0
+Bubalus_bubalis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0
+Mus_musculus 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 1 1 0 0 0 1 0 0 0
+Capra_aegagrus_hircus 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0
+Meleagris_gallopavo 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Macaca_mulatta 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0
+Mastomys_natalensis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Ovis_aries 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+Buffalo 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Pan_troglodytes 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 1 0 0 0 0 0 0 0 0
+;
+end;
diff --git a/Trees and Matrices/oral_choTangle.tre → Trees and Matrices/oral_tangle.tre b/Trees and Matrices/oral_choTangle.tre → Trees and Matrices/oral_tangle.tre