|
Arbre moins cohérent |
ElisaM
31 Mar 2021 8:05
Non evaluated contribution |
Bonjour,
j'ai trouvé mon groupe d'étude et mon groupe extérieur et je fais plusieurs test d'arbre pour voir s'il sont logiques et s'ils sont possible à étudier.
Après quelques recherche, j'arrive sur cet arbre ci dessous.
Il me semble peu juste car les Pélagibacter (groupe étude) ont une branche en commun avec des Rhodospirilla.
NEWICK TREE MANIPULATION
+------------------------+ BPARTT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+--+ 0.134000
| +------------------------------+ BPAHCC2-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
|
| +-----------------+ BPARAA2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+------+ 0.776000 |
| | +--------+ 0.858000-------+ BPARAK1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | +--------+ 0.885000
| | +--------------+ 0.934000 +---------+ BPARAA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | |
+--------+ 0.455000---+ 0.000000 +-------------------+ BPARA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
| | |
| | +----------------------+ BPARAG1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| |
| +------------------------------+ BPAHCC1-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
+--------------------+ 0.958000
| | +-------------------+ BPARRT2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +-------+ 0.114000-+ BPARRT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+----------------+ 0.965000 | | +-------+ 0.713000
| | +---+ 0.000000 +-----------------------------+ BPARRO1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +------------------------------------------+ BPARRN1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+---------+ 0.922000 |
| | +-----------+ BPARR1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
| |
| | +---------------------+ BPAPPC1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| +-----+ 0.751000
| +-------------------------------------------------------------+ BPAPPC3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
=|
| +---+ BPAPP1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
| +---+ 0.802000
| +---------------------------------------------------+ 1.000000------------------------+ BPAPP2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
| | |
| | | OMRGCv2-9592050-Traduction-10-498-sens-indirect
+---------+ 0.953000
| +----------+ BPAPPC2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| |
+------------------------+ 0.951000 +-----+ BPAPu1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
+-------------+
+-+ BPAPP3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
|------------------------------------|-----------------------------------|------------------------------------|---
0 0.2 0.4 0.6
substitutions/site
|
Meglecz20CTES
31 Mar 2021 11:18
Game master |
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ElisaM
8 Apr 2021 16:48
Non evaluated contribution |
Merci beaucoup,
Le nombre d'individu des deux groupes est-il suffisant ?
Merci
Cordialement
Elisa Mante
|
Meglecz20CTES
9 Apr 2021 11:16
Game master |
Bonjour Élisa,
Vu que vous n’avez pas beaucoup de hits dans le groupe d’étude, c’est OK pour le nombre des séquences.
Par contre les arbres ne sont toujours pas bien enracinés.
Bon travail,
Emese Meglecz
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ElisaM
15 Apr 2021 10:47
Non evaluated contribution |
Je n'arrive pas à l'enraciner avec le logiciel Newick tree manipulation.
J'ai regardé plusieurs fois la vidéo sur l'abre et plus particulièrement où vous m'avez dit mais lorsque je met "BPAPPC1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter BPAHCC1-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales" par exemple dans la barre de Root the tree on the following cela ne change pas l'arbre.
Avez vous une autre facon de faire par exemple?
(((((((((BPARTT1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.140370,
BPAHCC2_Bacteria_Proteobacteria_Alphaproteobacteria_Holosporales:0.173537)
0.107000:0.014767,
(((BPARAA2_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.095679,
(BPARAK1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.047078,
BPARAA1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.056574)
0.874000:0.045767)0.856000:0.050872,
BPARA1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirilla:0.111781)
0.946000:0.084368,
BPARAG1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.128465)
0.000000:0.030487)0.787000:0.038594,
BPAHCC1_Bacteria_Proteobacteria_Alphaproteobacteria_Holosporales:0.170947)
0.466000:0.046663,
((BPARRT2_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.109170,
(BPARRT1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.016503,
BPARRO1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.162976)
0.731000:0.046511)0.118000:0.038917,
BPARRN1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirill:0.230228)
0.000000:0.021976)0.964000:0.116129,
BPARR1_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirilla:0.062422)
0.968000:0.096155,
(BPAPPC1_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibacter:0.122686,
BPAPPC3_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibacter:0.343990)
0.769000:0.032583)0.888000:0.105501,
((BPAPP1_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibactera:0.023565,
BPAPP2_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibactera:0.162563)
0.823000:0.021843,OMRGCv2_9592050_Traduction_10-498_sens_indirect:0.000001)
0.999000:0.286280)0.973000:0.138098,
BPAPPC2_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibacter:0.062488)
0.950000:0.077115,
BPAPu1_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibactera:0.034665,
BPAPP3_Bacteria_Proteobacteria_Alphaproteobacteria_Pelagibactera:0.009544);
|
Meglecz20CTES
15 Apr 2021 18:32
Game master |
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ElisaM
16 Apr 2021 9:47
Non evaluated contribution |
Bonjour,
Grâce à votre vidéo j'ai réussi à faire cela mais il me semble qu'il n'est pas bon non plus. Je travaille le soir mais je vais essayé de demander à mon patron de prendre mon lundi soir pour pouvoir assister à votre séance zoom
+------------------------+ BPAPPC3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
|
| +-----------------+ BPAPPC1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| |
| | +-------------------+ BPARTT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | +-+ 0.134000
| | | +------------------------+ BPAHCC2-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
| | |
=| | | +-------------+ BPARAA2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | +-----+ 0.776000 |
| | | | +-------+ 0.858000---+ BPARAK1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | | | +-----+ 0.885000
| | | | +-----------+ 0.934000 +-------+ BPARAA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | | | |
| | +------+ 0.455000+ 0.000000 +---------------+ BPARA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
| | | | |
+------------------------+ 0.751000 | | +------------------+ BPARAG1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +------------------------+ BPAHCC1-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
| +---------------+ 0.958000
| | | +---------------+ BPARRT2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | |
| | | +----+ 0.114000 BPARRT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| +-------------+ 0.965000 | | +------+ 0.713000
| | | +---+ 0.000000 +----------------------+ BPARRO1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | |
| | | +--------------------------------+ BPARRN1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +--------+ BPARR1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
+----+ 0.922000
| +---+ BPAPP1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
| +--+ 0.802000
| +----------------------------------------+ 1.000000-----------------+ BPAPP2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
| | |
| | | OMRGCv2-9592050-Traduction-10-498-sens-indirect
+--------------+ 0.953000
| +--------+ BPAPPC2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| |
+-------------------+ 0.951000 +----+ BPAPu1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
+----------+
++ BPAPP3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
|-----------------------------------|-----------------------------------|------------------------------------|----
0 0.25 0.5 0.75
substitutions/site
|
Meglecz20CTES
17 Apr 2021 15:30
Game master |
Bonjour Élisa,
Concentrez sur le nœud qui regroupe toutes vos séquences de groupe extérieur : C’est avec la robustesse 0.965.
Prenez l’identifiant d’une séquence de chaque côté de ce nœud pour déplacer la racine.
Si le souci persiste, je vais faire un enregistrement vidéo pour vous montrer comment faire.
Bon travail,
Emese Meglecz
|
ElisaM
19 Apr 2021 12:09
Non evaluated contribution |
Bonjour,
Je crois que j'ai réussi :
+------------------------+ BPARTT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+--+ 0.107000
| +------------------------------+ BPAHCC2-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
|
| +----------------+ BPARAA2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+------+ 0.787000 |
| | +--------+ 0.856000-------+ BPARAK1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | +-------+ 0.874000
| | +--------------+ 0.946000 +----------+ BPARAA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | | |
+-------+ 0.466000---+ 0.000000 +-------------------+ BPARA1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
| | |
| | +----------------------+ BPARAG1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| |
| +------------------------------+ BPAHCC1-Bacteria-Proteobacteria-Alphaproteobacteria-Holosporales
+--------------------+ 0.964000
| | +-------------------+ BPARRT2-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +------+ 0.118000-+ BPARRT1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
+--------+ 0.968000 | | +-------+ 0.731000
| | +---+ 0.000000 +-----------------------------+ BPARRO1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| | |
| | +----------------------------------------+ BPARRN1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirill
| |
| +----------+ BPARR1-Bacteria-Proteobacteria-Alphaproteobacteria-Rhodospirilla
=|
| +---------------------+ BPAPPC1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| +-----+ 0.769000
| | +-------------------------------------------------------------+ BPAPPC3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| |
| | +---+ BPAPP1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
+--------+ 0.888000 +---+ 0.823000
| +---------------------------------------------------+ 0.999000-----------------------+ BPAPP2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
| | |
| | | OMRGCv2-9592050-Traduction-10-498-sens-indirect
+------------------+ 0.973000
| +----------+ BPAPPC2-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibacter
| |
+------------------------+ 0.950000 +-----+ BPAPu1-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
+-------------+
++ BPAPP3-Bacteria-Proteobacteria-Alphaproteobacteria-Pelagibactera
|-----------------------------------|-----------------------------------|------------------------------------|----
0 0.2 0.4 0.6
substitutions/site
|
Meglecz20CTES
19 Apr 2021 19:07
Game master |
|