PhylogÃ©nie Et Evolution Du Comportement Social Chez Les Blattes ...

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Ev o l u t i o n d u c o m p o r t e m e n t s o c i a lCo m m a n d e sCommandes utilisées lors des différentes analyses réalisées à partir d’un alignement dynamique(POY) ou statique. <strong>Les</strong> noms en italique correspondent à des noms de fichiers, des nomsd’espèces ou des variables.§§Analyse de parcimonie (POY) :Commandes relatives à la lecture et l’importation de données :set (log:“fichier.log”)read (“fichiers.txt”, “fichiers.ss”)transform (tcm:“fichier.txt”)read (prealigned:(“fichiers.fas”, tcm:(1,1)))read (custom_alphabet:(“fichier.txt”, “fichier.cout”, orientation:false, init3D:false))read (“fichier.tre”)set (root:“taxon”)select (terminals, files:(“fichier.tax”))report (data, cross_references)report (seq_stats:all)Commandes relatives à la recherche des arbres :build (all, 100)swap (all)report (timer:“nom”)fuse (iterations: 300, swap (all))report (treestats)select ()perturb (iterations:10, ratchet:(0.15,3))378
An n e x e sCommandes relatives à l’export des résultats :report (asciitrees)report (“fichier”, graphtrees)report (“fichier_con”, graphconsensus)report (“fichier.tre”, trees:(total))§§Analyse de parcimonie (PAUP) :outgroup taxon;pset opt=acctran;cstatus;set criterion=parsimony maxtrees=200 increase=auto autoinc=200;hsearch start=stepwise addseq=random nreps=1000 hold=5 swap=tbr;savetrees / brlens=yes file=fichier.tre replace=yes root=yes;contree / strict=yes save file=fichier_con.tre replace=yes;bootstrap nreps=1000 search=heuristic conlevel=50 grpfreq=yes keepall=notreefile=fichier_bootstrap.tre replace=yes brlens=yes search=heuristic/ addseq=randomnrep=1 swap=tbr;§§Analyse en maximum de vraisemblance (PHYML) :Model of nucleotide substitution = GTRBase frequency estimates = MLProportion of invariable sites = estimatedNumber of substitution rate categories = 6Gamma distribution parameter = estimatedInput tree = BIONJNon parametric bootstrap analysis = yes (1000 replicates)§§Analyse bayesienne (MrBayes) :set partition=nom autoclose=yes nowarn=yes;outgroup taxon;lset applyto=(all) nst=6 rates=invgamma;unlink Tratio=(all) Revmat=(all) statefreq=(all) shape=(all) pinvar=(all);mcmc ngen=1000000 samplefreq=100 printfreq=10000 nchains=4 savebrlens=yesfilename=fichier;379
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UFR des Sciences de la VieEcole Doc
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Je remercie toutes les personnes av
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Ta b l e d e s Mat i è r e sRe m e
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Données moléculaires sans les sé
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Ch a p i t r e V : Di s c u s s i o
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Figure 3.10 : Analyse cladistique d
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Li s t e d e s Ta b l e au xTableau
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In t r o d u c t i o nNothing in bi
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Ev o l u t i o n d u c o m p o r t
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I. An a ly s e d u c o n t e x t e
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II. Mat é r i e l s e t m é t h o
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ABCDEGHFJIK
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III. Réversibilité, c o n t r a i
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CHAPITRE IVEv o l u t i o n d e s c
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V. Dis c u s s ion g é n é r a l
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Ré f é r e n c e s b i b l i o g
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ANNEXE IDéf i n i t i o n s deq u
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ANNEXE IIPr o t o c o l e d’ex t
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ANNEXE IIILeg e n d r e et al . (Bi
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An n e x e sAbstractA new method is
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An n e x e sexpressed in such non-s
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An n e x e sanother species would a
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An n e x e sMolecular data for all
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An n e x e sevolutionary ecological
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An n e x e sThe comparison of the t
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An n e x e sDefining and including
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An n e x e s“avoiding” acts (GD
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An n e x e sGautier JY, Deleporte P
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An n e x e sMcLennan DA, Brooks DR,
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An n e x e sWenzel JW. 1993. Applic
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An n e x e sTable 1: PCR primers na
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An n e x e sTable 4: Phylogenetic a
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An n e x e sPhortioeca nimbataP.n.
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An n e x e sSchultesia lampyridifor
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An n e x e sSpecies 1 = outgroupInd
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An n e x e sAnalysis AEublaberus di
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Page 346 and 347: Ev o l u t i o n d u c o m p o r t
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PhylogÃ©nie Et Evolution Du Comportement Social Chez Les Blattes ...

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