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BCM-2003-A
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Envoyée par : Autre
Répondue par : Béatrice Roure
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2008-02-12
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Question
#475
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have couple of questions regarding the TP:
a) pg 20, we are asked to make a table to compare the results between PAUP
and PHyml( length,likelihood and monophyletics). Now for the PAUP and PHYML
do we need to do this for the 3 sets of data( 4genes, adn and aa) and all
the models (GTR,JC,f81,k2p,hky85)???
b) also for the PHYML , I wasnt' abe to see the lenth of the tree, is this
is recorded in a file? Because I checked all of them and didn't find it.
Also should we use only the "gamma distribution with 4 categories"(page 15)
when we compare the phyml with PAUP?
c) page 20, 3rd question: for the same set of data and same model , compare
the length of the tree by the method distance and parcimony: (again as I
have aske in part a) ) Do we need to do this comparison for the 3 sets of
data and for each of the 5 models(GTR,JC,f81,k2p,hky85) ?
these are the questions for now, I'll email you more tomorrow.
THank you
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Réponse
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Bonjour,
a) et c) Comme il est precise page 16, Il s'agit d'une synthese des resultats des 3 TPs de phylogenie. L'inference par maximum de vraisemblance etant longue, il faut tenir compte des resultats des 2 premieres seances pour justifier et limiter les inferences necessaires a celles qui ont ete faites pendant le dernier TP (PAUP: pages 6 a 10, PhyML: page 13 a 15)
b) La taille de l'arbre doit etre calculee a partir des longueurs de branches
Beatrice
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