Site undergoing maintenance! No connection possible during this time!

Forum "Analyse phylogénétique"

Thread subject: Re enracinement de l'arbre (issus de la matrice de distance)

[ Return to forums ]
Re enracinement de l'arbre (issus de la matrice de distance)
Vincent-Marine
29 Mar 2017 9:23
Non evaluated contribution

Bonjour,

qq soucis avec le re enracinement ERROR: Outgroup's LCA is tree's root - cannot reroot. Try -l. 

 

 

 

Arbre phyML avec 5. Tree Rendering Set. donc pas de valeur des noeud

       ,---+ BPGAAM1 Bacteria Proteobacteria Gammaproteobacteria Alteromonada                       
       |                                                                                            
       |   ,--+ BPGPPP1 Bacteria Proteobacteria Gammaproteobacteria Pseudomonada                    
       | ,-+                                                                                        
       |,+ '-+ BPGPPS1 Bacteria Proteobacteria Gammaproteobacteria Pseudomonada                     
   ,---+||                                                                                          
   |   ||'---+ BPG1 Bacteria Proteobacteria Gammaproteobacteria E-value2e-110                       
   |   ,+                                                                                           
   |   ||,--+ BPGOHC1 Bacteria Proteobacteria Gammaproteobacteria Oceanospiril                      
   |   |'+                                                                                          
   |   | '-+ BPGOHH1 Bacteria Proteobacteria Gammaproteobacteria Oceanospiril                       
   |   '                                                                                            
   |   | ,---+ BPGEED1 Bacteria Proteobacteria Gammaproteobacteria Enterobacter                     
   |   | |                                                                                          
   |   | |    , BPGVVS2 Bacteria Proteobacteria Gammaproteobacteria Vibrionales                     
   |   '-+,---+                                                                                     
   |     ||   ' BPGVVS1 Bacteria Proteobacteria Gammaproteobacteria Vibrionales                     
 ,-+     ||                                                                                         
 | |     '+  ,--+ BPGAAC1 Bacteria Proteobacteria Gammaproteobacteria Alteromonada                  
 | |      | ,+                                                                                      
 | |      | |'---+ BPGAAA1 Bacteria Proteobacteria Gammaproteobacteria Aeromonadale                 
 | |      '-+                                                                                       
 | |        | ,--+ BPGCCR1 Bacteria Proteobacteria Gammaproteobacteria Chromatiales                 
 | |        | |                                                                                     
 | |        '-+   ,-+ BPGPPR1 Bacteria Proteobacteria Gammaproteobacteria Pasteurellal              
 | |          '---+                                                                                 
 | |              '-+ BPGPPP2 Bacteria Proteobacteria Gammaproteobacteria Pasteurellal              
 | |                                                                                                
 | |         ,+ TO82D 6183060 Traduction 1-966 sens indirect                                        
 | '---------+                                                                                      
=+           ' BPGS1 Bacteria Proteobacteria Gammaproteobacteria SAR86 cluster                      
 |                                                                                                  
 | ,-----------+ BCOL1 Bacteria Cyanobacteria Oscillatoriales Leptolyngbya E-valu                   
 | |                                                                                                
 | | ,-------+ BPPPe1 Bacteria Planctomycetes Planctomycetacia Planctomycetales                     
 | | |                                                                                              
 | | |    ,----------------+ BSSSSS1 Bacteria Synergistetes Synergistia Synergistales Synergi       
 | | |    |                                                                                         
 | | |  ,-,--------+ BA1 Bacteria Armatimonadetes E-value3e-64 Bacteria Armatimonade                
 | | |  | '                                                                                         
 | | |  , '----------+ BCCCD1 Bacteria Chrysiogenetes Chrysiogenales Chrysiogenaceae De             
 | | |  |                                                                                           
 | | |  | ,-------+ BFCTTS1 Bacteria Firmicutes Clostridia Thermoanaerobacterales Th                
 '-+ |  '-+                                                                                         
   | |  | '----------+ BDDD1 Bacteria Deferribacteres Deferribacterales Deferribacterac             
   | |  |                                                                                           
   | |  |   ,------------+ BCCCC1 Bacteria Chitinivibrionia Chitinivibrionales Chitinivibri         
   | | ,+ ,-+                                                                                       
   | | ||,+ '-----------+ BSSSS1 Bacteria Spirochaetes Spirochaetales Spirochaetaceae Spir          
   | | ||||                                                                                         
   | | |||'-----------+ BGGGG1 Bacteria Gemmatimonadetes Gemmatimonadales Gemmatimonadac            
   | | |||                                                                                          
   | | ||| ,-----------+ BPDDDD2 Bacteria Proteobacteria Deltaproteobacteria Desulfovibri           
   | | ||| |                                                                                        
   | | ||| |  ,------+ BCCCC2 Bacteria Chloroflexi Chloroflexales Chloroflexaceae Chlor             
   '-+ |'+ |  |                                                                                     
     | | | |  |             , BPBMMM1 Bacteria Proteobacteria Betaproteobacteria Methylophilal      
     | | | |  |           ,-+                                                                       
     | | | |  |           | '-+ BPBMu1 Bacteria Proteobacteria Betaproteobacteria Methylophilale    
     | | | |  |        ,--+                                                                         
     | | | |  |        |  | ,-----+ BPBNNK1 Bacteria Proteobacteria Betaproteobacteria Neisseriales 
     | | '-+  |        |  '-+                                                                       
     | |   ,--+    ,---+    '-----+ BPB1 Bacteria Proteobacteria Betaproteobacteria E-value3e-56 Ba 
     | |   |  |    |   |                                                                            
     | |   |  |    |   '-----+ BPGMMM1 Bacteria Proteobacteria Gammaproteobacteria Methylococca     
     |,+   |  |  ,-+                                                                                
     |||   |  |  | |     ,-----+ BPAM1 Bacteria Proteobacteria Alphaproteobacteria Micavibrio E-v   
     |||   |  |  | |  ,--+                                                                          
     |||   |  |  | '--+  '-----+ BPARuE1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill   
     |||   |  '--+    |                                                                             
     |||   '     |    '-----+ BPARRR1 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale      
     |||   |     |                                                                                  
     |||   |     |          ,-+ BPZMMM1 Bacteria Proteobacteria Zetaproteobacteria Mariprofundal    
     |||   |     '----------+                                                                       
     |||   |                '---+ BPZ1 Bacteria Proteobacteria Zetaproteobacteria E-value7e-57 Ba   
     |||   |                                                                                        
     '+|   |   ,--------+ BE1 Bacteria Elusimicrobia E-value8e-58 Bacteria Elusimicrobia            
      ||   |   |                                                                                    
      ||   '---+        , BPES2 Bacteria Proteobacteria Epsilonproteobacteria Sulfurovum E          
      ||       '--------+                                                                           
      ||                ' BPES1 Bacteria Proteobacteria Epsilonproteobacteria Sulfurovum E          
      ||                                                                                            
      |'--------+ BA2 Bacteria Acidobacteria E-value2e-59 Bacteria Acidobacteria                    
      |                                                                                             
      |   ,--------+ BTTTT1 Bacteria Thermodesulfobacteria Thermodesulfobacteriales T               
      | ,-+                                                                                         
      | | '-------+ BPDSSD1 Bacteria Proteobacteria Deltaproteobacteria Syntrophobac                
      '-+                                                                                           
        |  ,-----+ BN1 Bacteria Nitrospirae E-value6e-67 Bacteria Nitrospirae gi 9                  
        '--+                                                                                        
           '--------+ BPDDDD1 Bacteria Proteobacteria Deltaproteobacteria Desulfobacte              
                                                                                                    
 |-----|-----|-----|-----|-----|---                                                                 
 0  0.25   0.5  0.75     1  1.25                                                                    
 substitutions/site   

Format Tree in Newick format avec Arbe phml . Phylogeny Set. Donc pas re enracine mais  impossible ERROR: Outgroup's LCA is tree's root - cannot reroot. Try -l. 

(((((((BA2_Bacteria_Acidobacteria_E-value=2e-59_Bacteria_Acidobacteria:0.391091,
(((BTTTT1_Bacteria_Thermodesulfobacteria_Thermodesulfobacteriales_T:0.370200,
BPDSSD1_Bacteria_Proteobacteria_Deltaproteobacteria_Syntrophobac:0.327450)
0.120000:0.077818,
(BN1_Bacteria_Nitrospirae_E-value=6e-67_Bacteria_Nitrospirae_gi_9:0.249962,
BPDDDD1_Bacteria_Proteobacteria_Deltaproteobacteria_Desulfobacte:0.383642)
0.585000:0.120327)0.478000:0.101668,
((((BPGAAM1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada:0.175911,
((((BPGPPP1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada:0.104437,
BPGPPS1_Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonada:0.064711)
0.922000:0.070793,
BPG1_Bacteria_Proteobacteria_Gammaproteobacteria_E-value=2e-110:0.156996)
0.796000:0.058046,
(BPGOHC1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril:0.126228,
BPGOHH1_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospiril:0.072023)
0.908000:0.057845)0.743000:0.030162,
(BPGEED1_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacter:0.168461,
((BPGVVS2_Bacteria_Proteobacteria_Gammaproteobacteria_Vibrionales:0.015938,
BPGVVS1_Bacteria_Proteobacteria_Gammaproteobacteria_Vibrionales:0.012670)
0.988000:0.152305,
((BPGAAC1_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonada:0.133783,
BPGAAA1_Bacteria_Proteobacteria_Gammaproteobacteria_Aeromonadale:0.171894)
0.561000:0.025879,
(BPGCCR1_Bacteria_Proteobacteria_Gammaproteobacteria_Chromatiales:0.131433,
(BPGPPR1_Bacteria_Proteobacteria_Gammaproteobacteria_Pasteurellal:0.092663,
BPGPPP2_Bacteria_Proteobacteria_Gammaproteobacteria_Pasteurellal:0.088401)
0.994000:0.181451)0.651000:0.067771)0.861000:0.065852)0.138000:0.036427)
0.937000:0.089559)0.107000:0.022170)0.948000:0.153826,
(TO82D_6183060_Traduction_1-966_sens_indirect:0.056432,
BPGS1_Bacteria_Proteobacteria_Gammaproteobacteria_SAR86_cluster:0.000001)
1.000000:0.401836)0.955000:0.185869,
BCOL1_Bacteria_Cyanobacteria_Oscillatoriales_Leptolyngbya_E-valu:0.484769)
0.837000:0.068518,
BPPPe1_Bacteria_Planctomycetes_Planctomycetacia_Planctomycetales:0.344662)
0.853000:0.049404)0.637000:0.028124)0.816000:0.042485,
((BSSSSS1_Bacteria_Synergistetes_Synergistia_Synergistales_Synergi:0.740060,
(BA1_Bacteria_Armatimonadetes_E-value=3e-64_Bacteria_Armatimonade:0.370473,
BCCCD1_Bacteria_Chrysiogenetes_Chrysiogenales_Chrysiogenaceae_De:0.437334)
0.090000:0.030555)0.798000:0.058326,
(BFCTTS1_Bacteria_Firmicutes_Clostridia_Thermoanaerobacterales_Th:0.349029,
BDDD1_Bacteria_Deferribacteres_Deferribacterales_Deferribacterac:0.447804)
0.861000:0.070986)0.672000:0.026976)0.901000:0.073919,
((BCCCC1_Bacteria_Chitinivibrionia_Chitinivibrionales_Chitinivibri:0.526892,
BSSSS1_Bacteria_Spirochaetes_Spirochaetales_Spirochaetaceae_Spir:0.499011)
0.770000:0.097720,
BGGGG1_Bacteria_Gemmatimonadetes_Gemmatimonadales_Gemmatimonadac:0.488886)
0.627000:0.029707)0.812000:0.047807,
BPDDDD2_Bacteria_Proteobacteria_Deltaproteobacteria_Desulfovibri:0.545196)
0.519000:0.033258,
(BCCCC2_Bacteria_Chloroflexi_Chloroflexales_Chloroflexaceae_Chlor:0.265787,
(((((BPBMMM1_Bacteria_Proteobacteria_Betaproteobacteria_Methylophilal:0.010819,
BPBMu1_Bacteria_Proteobacteria_Betaproteobacteria_Methylophilale:0.085594)
0.499000:0.052562,
(BPBNNK1_Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales:0.256730,
BPB1_Bacteria_Proteobacteria_Betaproteobacteria_E-value=3e-56_Ba:0.264322)
0.632000:0.058341)0.954000:0.153009,
BPGMMM1_Bacteria_Proteobacteria_Gammaproteobacteria_Methylococca:0.257213)
0.948000:0.177244,
((BPAM1_Bacteria_Proteobacteria_Alphaproteobacteria_Micavibrio_E-v:0.277656,
BPARuE1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.246644)
0.804000:0.111918,
BPARRR1_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiale:0.256126)
0.885000:0.148318)0.416000:0.077036,
(BPZMMM1_Bacteria_Proteobacteria_Zetaproteobacteria_Mariprofundal:0.085509,
BPZ1_Bacteria_Proteobacteria_Zetaproteobacteria_E-value=7e-57_Ba:0.174602)
1.000000:0.461674)0.911000:0.094683)0.938000:0.133772)0.943000:0.152986,
BE1_Bacteria_Elusimicrobia_E-value=8e-58_Bacteria_Elusimicrobia:0.374331)
1.000000:0.377436,
BPES2_Bacteria_Proteobacteria_Epsilonproteobacteria_Sulfurovum_E:0.011223,
BPES1_Bacteria_Proteobacteria_Epsilonproteobacteria_Sulfurovum_E:0.016453);

 

Vincent-Marine
29 Mar 2017 9:34
Non evaluated contribution

Du coup nous rédigons sans les valeurs des noeuds. Mais cela est-il vraiment correcte? Ce soucis avec le re-enracinement pose vraiment soucis. Le format      5. Tree Rendering Set.    qui nous permet de bien re-enraciner l'arbre quand expoté en     Newick     et le logiciel de re-enracinement ne nous donne pas de valeur non plus.