Source Code for Package ete2.phylomedb

 1  __VERSION__="ete2-2.0rev90"  
 2  # #START_LICENSE########################################################### 
 3  # 
 4  # Copyright (C) 2009 by Jaime Huerta Cepas. All rights reserved.   
 5  # email: jhcepas@gmail.com 
 6  # 
 7  # This file is part of the Environment for Tree Exploration program (ETE).  
 8  # http://ete.cgenomics.org 
 9  #   
10  # ETE is free software: you can redistribute it and/or modify it 
11  # under the terms of the GNU General Public License as published by 
12  # the Free Software Foundation, either version 3 of the License, or 
13  # (at your option) any later version. 
14  #   
15  # ETE is distributed in the hope that it will be useful, 
16  # but WITHOUT ANY WARRANTY; without even the implied warranty of 
17  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
18  # GNU General Public License for more details. 
19  #   
20  # You should have received a copy of the GNU General Public License 
21  # along with ETE.  If not, see <http://www.gnu.org/licenses/>. 
22  # 
23  # #END_LICENSE############################################################# 
24   
25   
26  species_ages = {} 
27   
28  _humanv1 = { 
29  # Basal eukariotes 
30  "Ath":10, # Arabidopsis thaliana 
31  "Cre":10, 
32  "Pfa":10, 
33  "Pyo":10, 
34  "Ddi":10, 
35  "Gth":10, 
36  "Lma":10, # leismania 
37  "Pte":10, 
38   
39  # Fungi 
40  "Ago":9, 
41  "Cal":9, 
42  "Cgl":9, 
43  "Cne":9, 
44  "Dha":9, 
45  "Ecu":9, 
46  "Gze":9, 
47  "Kla":9, 
48  "Ncr":9, 
49  "Sce":9, # S.cerevisiae 
50  "Spb":9, 
51  "Yli":9, 
52   
53  # metazoa non chordates 
54  "Aga":8, # Anopheles 
55  "Dme":8, # Drosophila melanogaster 
56  "Ame":8, # Apis meliferae 
57  "Cel":8, # Caenorabditis elegans 
58  "Cbr":8, # Caenorabditis brigssae 
59   
60  # chordates non vertebrates 
61  "Cin":7, # Ciona intestinalis 
62   
63  # vertebrates non tetrapodes 
64  "Dre":6, # Danio rerio 
65  "Tni":6, # Tetraodom 
66  "Fru":6, # Fugu rubripes 
67   
68  # tetrapodes non birds nor mammals 
69  "Xtr":5, # Xenopus 
70   
71  # birds 
72  "Gga":4, # Chicken 
73   
74  # Mammals non primates 
75  "Mdo":3, # Monodelphis domestica 
76  "Mms":3, # Mouse 
77  "Rno":3, # Rat 
78  "Cfa":3, # Dog 
79  "Bta":3, # Cow 
80   
81  # primates non hominids 
82  "Ptr":2, # chimp 
83  "Mmu":2, # Macaca 
84   
85  # hominids 
86  "Hsa":1, # human 
87  } 
88  species_ages["human_phylome"] = _humanv1 
89