Je crois et j'espere toucher au but.
Est-il possible d'enraciner l'arbre comme cela?
+--------------------------+ BPB1-E-value3e-84-Bacteria-Proteobacteria-Betaprot +----------+ 0.88 | +---------------------------------+ BPZ1-E-value7e-84-Bacteria-Proteobacteria-Zetaprot | +--------+ 0.68 +-------+ BPECCC1-E-value6e-82-Bacteria-Proteobacteria-Epsil | | +--------+ 0.84 | +--------------------+ 0.99 +----------+ BPGEEB1-E-value8e-83-Bacteria-Proteobacteria-Gamma +--------+ 0.88 | | | +----+ BPGEMP1-E-value3e-84-Bacteria-Proteobacteria-Gamma | | | +---------------------+ BPG1-E-value6e-92-Bacteria-Proteobacteria-Gammapro | | | BPA1-E-value5e-164-Bacteria-Proteobacteria-Alphapr | +---------+ | ++ 0.99 | BPAP1-E-value3e-164-Bacteria-Proteobacteria-Alphap | || | +-------------------------------------------------------------------------++0.00-------+ OMRGCv2-11017080-Translation-168-1070-indirect-str | | | | | +-------------+ BPA2-E-value1e-146-Bacteria-Proteobacteria-Alphapr | | | | +---------+ BPAEEPE1-E-value3e-92-Bacteria-Proteobacteria-Alph | | +-----------+ 0.98 | | | +----------+ BPAKKK2-E-value2e-92-Bacteria-Proteobacteria-Alpha | | +----+ 0.20 +------------------------------------+ 0.30 | | | +-----------+ BPAEEE1-E-value1e-95-Bacteria-Proteobacteria-Alpha | | | | +--------------+ 0.99 | | | +---------+ 0.94 +--------+ BPAS1-E-value2e-93-Bacteria-Proteobacteria-Alphapr | | | | | | | | +--------+ 0.87 +----------------------------------+ BPAKKK1-E-value5e-89-Bacteria-Proteobacteria-Alpha | | | | | | | | ++ 0.55 +----------------------------------------------------------+ BPARG1-E-value9e-89-Bacteria-Proteobacteria-Alphap | | | || | | | |+---------------------------+ BPARRR1-E-value1e-90-Bacteria-Proteobacteria-Alpha | | | | | | | | +------------------------+ BPARAAA1-E-value9e-86-Bacteria-Proteobacteria-Alph | | | | +----+ 0.29 | | | | | +-------------------------+ BPASSO1-E-value6e-90-Bacteria-Proteobacteria-Alpha | | | | | | | | | +----+ 0.85 +---------------------+ BPA5-E-value4e-92-Bacteria-Proteobacteria-Alphapro | | | | | | +--+ 0.71 | | | | | | | +-----------------------------------+ BPAHRT1-E-value9e-90-Bacteria-Proteobacteria-Alpha | | | +---+ 0.60 | | | +-----------+ 1.00 | | | +----+ 0.80 +------------------------+ BPA3-E-value7e-94-Bacteria-Proteobacteria-Alphapro | | | | | | +--------------+ 0.97 | | | |+---+ 0.38 +-------+ 0.84 +----------------+ BPARTN1-E-value3e-97-Bacteria-Proteobacteria-Alpha | | | || | | | | | || | +-------------------------+ BPARKAA1-E-value6e-101-Bacteria-Proteobacteria-Alp | | | || | | | | || | +-----+ BPA4-E-value2e-93-Bacteria-Proteobacteria-Alphapro | | | || | +--------------------------+ 1.00 =| | | || +------------+ 0.97 +------+ BPA6-E-value3e-91-Bacteria-Proteobacteria-Alphapro | | +------+ 0.81 0.62 | | | | | | +----------------------------+ BPARRM1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | | | | +-----------------+ BPA8-E-value1e-87-Bacteria-Proteobacteria-Alphapro | | | | | +----+ 0.47 | | | | | +----------+ 0.94----------+ BPASSS1-E-value3e-92-Bacteria-Proteobacteria-Alpha | | | | | | | | | | | +--------------------+ 0.99 +----------------+ BPASS1-E-value8e-92-Bacteria-Proteobacteria-Alphap | | | | | | | | | +-----------+ BPASSSS1-E-value1e-93-Bacteria-Proteobacteria-Alph | | +--------+ 0.84 | | | | | +------------------------------------------------------------+ BPA7-E-value1e-89-Bacteria-Proteobacteria-Alphapro | | | | | | | | +-------+ BPARRR2-E-value6e-87-Bacteria-Proteobacteria-Alpha | | | | +-----+ 0.69 | | | | +----------------+ 0.99+---------------+ BPARRT1-E-value8e-91-Bacteria-Proteobacteria-Alpha | +--------+ 0.90 | | | | | | +-------------------+ 0.98 +-------------------------+ BPARPP1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | +--------+ 0.92 +---------------+ BPAH1-E-value2e-91-Bacteria-Proteobacteria-Alphapr | | | | | +-------------------------+ BPAHM1-E-value1e-87-Bacteria-Proteobacteria-Alphap | | | +----------------------------------------+ BPA9-E-value6e-86-Bacteria-Proteobacteria-Alphapro | +------------------------------------+ BPOSSS1-E-value2e-83-Bacteria-Proteobacteria-Oligo |-------------------------------|------------------------------|-------------------------------|-------------------------------|-------------------- 0 0.25 0.5 0.75 1 substitutions/site
Non. La racine devrait être entre le groupe d’étude et le groupe extérieur.
Après avoir visionné la video je ne comprends pas pourquoi la technique ne fonctionne pas pour mon arbre
Je vais vous detailler ma démarche
Etape 1: Je lance mon arbre sur newick et obtiens
+------------------+ BPB1-E-value3e-84-Bacteria-Proteobacteria-Betaprot +------+ 0.88 | +-----------------------+ BPZ1-E-value7e-84-Bacteria-Proteobacteria-Zetaprot | +------+ 0.68 +-----+ BPECCC1-E-value6e-82-Bacteria-Proteobacteria-Epsil | | +-----+ 0.84 | +-------------+ 0.99+-------+ BPGEEB1-E-value8e-83-Bacteria-Proteobacteria-Gamma +-----+ 0.88 | | | +--+ BPGEMP1-E-value3e-84-Bacteria-Proteobacteria-Gamma +-------+ 0.30| | | +---------------+ BPG1-E-value6e-92-Bacteria-Proteobacteria-Gammapro | | | +--------------------------------------------------+ BPOSSS1-E-value2e-83-Bacteria-Proteobacteria-Oligo | | +------+ BPAEEPE1-E-value3e-92-Bacteria-Proteobacteria-Alph | +--------+ 0.98 | | +-------+ BPAKKK2-E-value2e-92-Bacteria-Proteobacteria-Alpha | +--+ 0.20 | | | +-------+ BPAEEE1-E-value1e-95-Bacteria-Proteobacteria-Alpha | | +----------+ 0.99 | +------+ 0.94 +-----+ BPAS1-E-value2e-93-Bacteria-Proteobacteria-Alphapr | | | | +-----+ 0.87 +-----------------------+ BPAKKK1-E-value5e-89-Bacteria-Proteobacteria-Alpha | | | | ++ 0.55+----------------------------------------+ BPARG1-E-value9e-89-Bacteria-Proteobacteria-Alphap | || | |+------------------+ BPARRR1-E-value1e-90-Bacteria-Proteobacteria-Alpha | | | | +----------------+ BPARAAA1-E-value9e-86-Bacteria-Proteobacteria-Alph | | +---+ 0.29 | | | +----------------+ BPASSO1-E-value6e-90-Bacteria-Proteobacteria-Alpha | | | | | +--+ 0.85+--------------+ BPA5-E-value4e-92-Bacteria-Proteobacteria-Alphapro | | | | +-+ 0.71 | | | | | +------------------------+ BPAHRT1-E-value9e-90-Bacteria-Proteobacteria-Alpha +---------------------------------------------------+ 1.00 +--+ 0.60 | | | | | | | +---+ 0.80 +-----------------+ BPA3-E-value7e-94-Bacteria-Proteobacteria-Alphapro | | | | | | +---------+ 0.97 | | | |+--+ 0.38 +----+ 0.84 +-----------+ BPARTN1-E-value3e-97-Bacteria-Proteobacteria-Alpha | | | || | | | | | || | +-----------------+ BPARKAA1-E-value6e-101-Bacteria-Proteobacteria-Alp | | | || | | | | || | +---+ BPA4-E-value2e-93-Bacteria-Proteobacteria-Alphapro | | | || | +------------------+ 1.00 | | | || +-------+ 0.97 +-----+ BPA6-E-value3e-91-Bacteria-Proteobacteria-Alphapro | | +---+ 0.810.62 | | | | | | +--------------------+ BPARRM1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | | | | +------------+ BPA8-E-value1e-87-Bacteria-Proteobacteria-Alphapro | | | | | +--+ 0.47 | | | | | +------+ 0.94-----+ BPASSS1-E-value3e-92-Bacteria-Proteobacteria-Alpha | | | | | | | | | | | +--------------+ 0.99 +-----------+ BPASS1-E-value8e-92-Bacteria-Proteobacteria-Alphap | 0.00 | | | | | | | | +-------+ BPASSSS1-E-value1e-93-Bacteria-Proteobacteria-Alph | | +------+ 0.84 | | | | +------------------------------------------+ BPA7-E-value1e-89-Bacteria-Proteobacteria-Alphapro | | | | | | | | +----+ BPARRR2-E-value6e-87-Bacteria-Proteobacteria-Alpha | | | | +---+ 0.69 | | | | +------------+ 0.99--------+ BPARRT1-E-value8e-91-Bacteria-Proteobacteria-Alpha | +-----+ 0.90 | | | +------+ 0.99 | | +------------+ 0.98 +-----------------+ BPARPP1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | | | +-----+ 0.92 +-----------+ BPAH1-E-value2e-91-Bacteria-Proteobacteria-Alphapr | | | | | | | +-----------------+ BPAHM1-E-value1e-87-Bacteria-Proteobacteria-Alphap | | | | | +----------------------------+ BPA9-E-value6e-86-Bacteria-Proteobacteria-Alphapro =| | | |---------+ BPA2-E-value1e-146-Bacteria-Proteobacteria-Alphapr | | | +-------+ OMRGCv2-11017080-Translation-168-1070-indirect-str | | BPA1-E-value5e-164-Bacteria-Proteobacteria-Alphapr | | BPAP1-E-value3e-164-Bacteria-Proteobacteria-Alphap |---------------------|---------------------|---------------------|---------------------|---------------------|----------------- 0 0.25 0.5 0.75 1 1.25 substitutions/site
Etape 1: J'enracine mon arbre sur un taxa du groupe extérieur pour obtenir un arbre similaire à la video ici
BPG1-E-value6e-92-Bacteria-Proteobacteria-Gammapro (surligné en jaune). J'obtiens alors:
| BPA1-E-value5e-164-Bacteria-Proteobacteria-Alphapr +---------+ ++ 0.99 | BPAP1-E-value3e-164-Bacteria-Proteobacteria-Alphap || +-----------------------------------------------------------------------++0.00-------+ OMRGCv2-11017080-Translation-168-1070-indirect-str | | | +-------------+ BPA2-E-value1e-146-Bacteria-Proteobacteria-Alphapr | | +---------+ BPAEEPE1-E-value3e-92-Bacteria-Proteobacteria-Alph | +-----------+ 0.98 | | +----------+ BPAKKK2-E-value2e-92-Bacteria-Proteobacteria-Alpha | +----+ 0.20 | | | +-----------+ BPAEEE1-E-value1e-95-Bacteria-Proteobacteria-Alpha | | +--------------+ 0.99 | +---------+ 0.94 +--------+ BPAS1-E-value2e-93-Bacteria-Proteobacteria-Alphapr | | | | +-------+ 0.87 +---------------------------------+ BPAKKK1-E-value5e-89-Bacteria-Proteobacteria-Alpha | | | | +-+ 0.55 +---------------------------------------------------------+ BPARG1-E-value9e-89-Bacteria-Proteobacteria-Alphap | | | | | +--------------------------+ BPARRR1-E-value1e-90-Bacteria-Proteobacteria-Alpha | | | | +-----------------------+ BPARAAA1-E-value9e-86-Bacteria-Proteobacteria-Alph | | +----+ 0.29 | | | +-----------------------+ BPASSO1-E-value6e-90-Bacteria-Proteobacteria-Alpha | | | | | +-----+ 0.85 +---------------------+ BPA5-E-value4e-92-Bacteria-Proteobacteria-Alphapro | | | | +--+ 0.71 | | | | | +----------------------------------+ BPAHRT1-E-value9e-90-Bacteria-Proteobacteria-Alpha | +--+ 0.60 | | +----------+ 1.00 | | | +---+ 0.80 +------------------------+ BPA3-E-value7e-94-Bacteria-Proteobacteria-Alphapro | | | | | | +-------------+ 0.97 | | | | +--+ 0.38 +-------+ 0.84 +----------------+ BPARTN1-E-value3e-97-Bacteria-Proteobacteria-Alpha | | | | | | | | | | | | | +-------------------------+ BPARKAA1-E-value6e-101-Bacteria-Proteobacteria-Alp | | | | | | | | | | | | +----+ BPA4-E-value2e-93-Bacteria-Proteobacteria-Alphapro | | | | | | +--------------------------+ 1.00 | | | | | +------------+ 0.97 +------+ BPA6-E-value3e-91-Bacteria-Proteobacteria-Alphapro | | +------+ 0.81 0.62 | | | | | | +---------------------------+ BPARRM1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | | | | +-----------------+ BPA8-E-value1e-87-Bacteria-Proteobacteria-Alphapro | | | | | +---+ 0.47 | | | | | +----------+ 0.94----------+ BPASSS1-E-value3e-92-Bacteria-Proteobacteria-Alpha | | | | | | | | | | | +-------------------+ 0.99 +---------------+ BPASS1-E-value8e-92-Bacteria-Proteobacteria-Alphap +--------+ 0.30 | | | | | | | | | +-----------+ BPASSSS1-E-value1e-93-Bacteria-Proteobacteria-Alph | | | +--------+ 0.84 | | | | | | +-----------------------------------------------------------+ BPA7-E-value1e-89-Bacteria-Proteobacteria-Alphapro | | | | | | | | | | +------+ BPARRR2-E-value6e-87-Bacteria-Proteobacteria-Alpha | | | | | +-----+ 0.69 | | | | | +----------------+ 0.99+--------------+ BPARRT1-E-value8e-91-Bacteria-Proteobacteria-Alpha | | +--------+ 0.90 | | | | | | | +-------------------+ 0.98 +-------------------------+ BPARPP1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | +----------+ 0.88 | | +-------+ 0.92 +---------------+ BPAH1-E-value2e-91-Bacteria-Proteobacteria-Alphapr | | | | | | | | | +-------------------------+ BPAHM1-E-value1e-87-Bacteria-Proteobacteria-Alphap | | | | | | | +---------------------------------------+ BPA9-E-value6e-86-Bacteria-Proteobacteria-Alphapro | | | | | +-----------------------------------------------------------------------+ BPOSSS1-E-value2e-83-Bacteria-Proteobacteria-Oligo | | | | +--------------------------+ BPB1-E-value3e-84-Bacteria-Proteobacteria-Betaprot =| | +---------+ 0.88 | | | +---------------------------------+ BPZ1-E-value7e-84-Bacteria-Proteobacteria-Zetaprot | | | | +--------+ 0.68 +--------+ BPECCC1-E-value6e-82-Bacteria-Proteobacteria-Epsil | | +-------+ 0.84 | +-------------------+ 0.99 +----------+ BPGEEB1-E-value8e-83-Bacteria-Proteobacteria-Gamma | | | +---+ BPGEMP1-E-value3e-84-Bacteria-Proteobacteria-Gamma | +----------+ BPG1-E-value6e-92-Bacteria-Proteobacteria-Gammapro |------------------------------|------------------------------|------------------------------|------------------------------|--- 0 0.25 0.5 0.75 1 substitutions/site
sur cet arbre nous distingons trés bien les alpha du groupe exterieur( alpha en orange) Il me suffit normalement d'enraciner en prennant un groupe du haut et un du bas. admettons les deux en jaune.
voila l'arbre que j'obtiens:
+-------------------+ BPB1-E-value3e-84-Bacteria-Proteobacteria-Betaprot +------+ 0.88 | +-------------------------+ BPZ1-E-value7e-84-Bacteria-Proteobacteria-Zetaprot | +------+ 0.68 +------+ BPECCC1-E-value6e-82-Bacteria-Proteobacteria-Epsil | | +-----+ 0.84 | +--------------+ 0.99+--------+ BPGEEB1-E-value8e-83-Bacteria-Proteobacteria-Gamma +------+ 0.88 | | | +--+ BPGEMP1-E-value3e-84-Bacteria-Proteobacteria-Gamma +-------+ 0.30 | | | +---------------+ BPG1-E-value6e-92-Bacteria-Proteobacteria-Gammapro | | | +------------------------------------------------------+ BPOSSS1-E-value2e-83-Bacteria-Proteobacteria-Oligo | | +------+ BPAEEPE1-E-value3e-92-Bacteria-Proteobacteria-Alph | +---------+ 0.98 | | +-------+ BPAKKK2-E-value2e-92-Bacteria-Proteobacteria-Alpha | +--+ 0.20 | | | +--------+ BPAEEE1-E-value1e-95-Bacteria-Proteobacteria-Alpha | | +-----------+ 0.99 | +------+ 0.94 +-----+ BPAS1-E-value2e-93-Bacteria-Proteobacteria-Alphapr | | | | +------+ 0.87 +------------------------+ BPAKKK1-E-value5e-89-Bacteria-Proteobacteria-Alpha | | | | ++ 0.55 +------------------------------------------+ BPARG1-E-value9e-89-Bacteria-Proteobacteria-Alphap | || | |+--------------------+ BPARRR1-E-value1e-90-Bacteria-Proteobacteria-Alpha | | | | +-----------------+ BPARAAA1-E-value9e-86-Bacteria-Proteobacteria-Alph | | +---+ 0.29 | | | +-----------------+ BPASSO1-E-value6e-90-Bacteria-Proteobacteria-Alpha | | | | | +---+ 0.85+---------------+ BPA5-E-value4e-92-Bacteria-Proteobacteria-Alphapro | | | | +--+ 0.71 | | | | | +-------------------------+ BPAHRT1-E-value9e-90-Bacteria-Proteobacteria-Alpha +------------------------------------------------------+ 1.00 +--+ 0.60 | | | | | | | +--+ 0.80 +-----------------+ BPA3-E-value7e-94-Bacteria-Proteobacteria-Alphapro | | | | | | +----------+ 0.97 | | | |+--+ 0.38 +-----+ 0.84 +------------+ BPARTN1-E-value3e-97-Bacteria-Proteobacteria-Alpha | | | || | | | | | || | +------------------+ BPARKAA1-E-value6e-101-Bacteria-Proteobacteria-Alp | | | || | | | | || | +----+ BPA4-E-value2e-93-Bacteria-Proteobacteria-Alphapro | | | || | +-------------------+ 1.00 | | | || +--------+ 0.97 +-----+ BPA6-E-value3e-91-Bacteria-Proteobacteria-Alphapro | | +---+ 0.810.62 | | | | | | +---------------------+ BPARRM1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | | | | | | +------------+ BPA8-E-value1e-87-Bacteria-Proteobacteria-Alphapro | | | | | +--+ 0.47 | | | | | +-------+ 0.94-----+ BPASSS1-E-value3e-92-Bacteria-Proteobacteria-Alpha | | | | | | | | | | | +---------------+ 0.99 +-----------+ BPASS1-E-value8e-92-Bacteria-Proteobacteria-Alphap | 0.00 | | | | | | | | +--------+ BPASSSS1-E-value1e-93-Bacteria-Proteobacteria-Alph | | +------+ 0.84 | | | | +---------------------------------------------+ BPA7-E-value1e-89-Bacteria-Proteobacteria-Alphapro | | | | | | | | +----+ BPARRR2-E-value6e-87-Bacteria-Proteobacteria-Alpha | | | | +----+ 0.69 | | | | +------------+ 0.99----------+ BPARRT1-E-value8e-91-Bacteria-Proteobacteria-Alpha | +------+ 0.90 | | | | | | +-------------+ 0.98 +------------------+ BPARPP1-E-value9e-87-Bacteria-Proteobacteria-Alpha | | | | | =| | +-----+ 0.92 +-----------+ BPAH1-E-value2e-91-Bacteria-Proteobacteria-Alphapr | | | | | +------------------+ BPAHM1-E-value1e-87-Bacteria-Proteobacteria-Alphap | | | +-----------------------------+ BPA9-E-value6e-86-Bacteria-Proteobacteria-Alphapro | |----------+ BPA2-E-value1e-146-Bacteria-Proteobacteria-Alphapr | | | BPA1-E-value5e-164-Bacteria-Proteobacteria-Alphapr |-------+ | 0.99 | BPAP1-E-value3e-164-Bacteria-Proteobacteria-Alphap | +--------+ OMRGCv2-11017080-Translation-168-1070-indirect-str |----------------------|-----------------------|----------------------|----------------------|----------------------|----------- 0 0.25 0.5 0.75 1 1.25 substitutions/site
Je ne comprends pas pourquoi je n'arrive pas a enraciner mon arbre correctement
Bonjour,
Merci pour vos explications précises. Cela m’aide à comprendre votre erreur.
Si l’arbre n’est pas enraciné correctement, alors la racine sépare en deux soit le groupe d’étude, soit le groupe extérieur, tandis que l’outre groupe est bien délimité par un nœud.
Par exemple, dans l’arbre de l’étape 1 (Etape 1: Je lance mon arbre sur newick et obtiens), le groupe extérieur est clairement délimité par un nœud avec la robustesse 0.3. Tous les descendants de ce nœud sont les non-alpha, et tous les non-alpha descendent de ce nœud.
Le groupe d’étude est coupé en deux par la racine (deux séquences sont un côté de la racine, les autres sont sur l’autre).
Il faut donc focaliser sur le groupe extérieur dans votre cas, car c’est le groupe qui est bien regroupé sous un nœud.
Il faut indiquer à l’outil de la visualisation de l’arbre de l’annotathon ce noeud, pour qu’il place la racine entre ce nœud (groupe extérieur) et toutes les autres séquences (groupe d’étude).
Pour le faire, il faut un identifiant de chacune des deux branches qui descend de ce nœud. Autrement dit, il faut sélectionner deux séquences dont l’ancêtre le plus récent se trouve à ce nœud.
Votre erreur était de choisir une séquence de groupe d’étude et une autre de groupe extérieur ce qui place nécessairement mal la racine.
Bon travail, Emese Meglecz
CA FONCTIONNE !!!!!