rooted tree from PHYML analysis

[monkey79]

Hi there,

I want to access to evolutionary events of my trees. I know that firstly the tree must be rooted, but I had some problems. 

I have run PHYML in order to obtain gene trees in newick format, and rooted each trees. So the output from PHYML is: 

(((((((cin_04084:1.4393170460,*m_002441:2.4940764588)0.9320000000:0.4578453002,hs_154655:0.6314684547)0.4200000000:0.0572400724,(gac_01138:0.2826341773,tru_01294:0.2265643531)1.0000000000:0.6017368927)0.8180000000:0.0974985300,(((gal_00983:0.1067916112,hs_185513:0.3905341496)0.9610000000:0.1072801261,gac_06074:0.6318681781)0.6550000000:0.0328186725,lch_03590:0.1950692295)1.0000000000:0.4335788423)0.9580000000:0.1357738912,(gal_14009:0.2388334505,hs_198945:0.1473934714)1.0000000000:0.4461520716)0.9990000000:0.2643879102,(gal_01345:0.2650147919,lch_08848:0.2209999269)0.9620000000:0.1412696558)1.0000000000:0.4147717866,gac_09206:0.0846301058,tru_08264:0.0824025592);

the tree returned by PhyML is rooted and has *m_002441 as outgroup.

However, when I get to the point  where I want to run evolutionary events I get: Tree is not rooted.

Any help will be appreciated,

thanks

B

[Salvador Capella]

Hi Barbara,

I have executed the code below and I have realized your tree is not rooted.

from ete2 import PhyloTree

t = PhyloTree("""(((((((cin_04084:1.4393170460,*m_002441:2.4940764588)0.9320000000:0.4578453002,hs_154655:0.6314684547)0.4200000000:0.0572400724,(gac_01138:0.2826341773,tru_01294:0.2265643531)1.0000000000:0.6017368927)0.8180000000:0.0974985300,(((gal_00983:0.1067916112,hs_185513:0.3905341496)0.9610000000:0.1072801261,gac_06074:0.6318681781)0.6550000000:0.0328186725,lch_03590:0.1950692295)1.0000000000:0.4335788423)0.9580000000:0.1357738912,(gal_14009:0.2388334505,hs_198945:0.1473934714)1.0000000000:0.4461520716)0.9990000000:0.2643879102,(gal_01345:0.2650147919,lch_08848:0.2209999269)0.9620000000:0.1412696558)1.0000000000:0.4147717866,gac_09206:0.0846301058,tru_08264:0.0824025592);""")

t.show()

I'd like to suggest you to root the tree on this way.

myOutgroup = t.search_nodes(name = "*m_002441")[0]

t.set_outgroup(myOutgroup)

t.show()

Then, you can get your evolutionary events.

I know you could say to phyml, using the * symbol,  to use a giving sequence as root for the phylogenetic tree but in this cases, it looks like it didn't work.

Cheers,

S

[monkey79]

ok thanks

B