Problems with the tree format of MAP tree

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彭婷

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Sep 30, 2019, 11:15:18 AM9/30/19
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Dear Sir or Madam:
My name is Cynthia Peng and I am a PhD student from China. Recently I am studying how to use BAli-phy (bali-phy-3.4.1) with the guide of the instrctions.
I get the summary of the output with the command of "bp-analyze". However, I encounter a problem when I read the results. I found that the
majority consensus tree and MAP tree can not be opened by TreeView. And when I regard the MAP tree file as my input of PAML/CodeML analysis,
it also reports an error and says that a seq which exists in my alignment file but is missing in the tree. For example, the "Agrobacterium"
in the following MAP tree file will be regared as the missing seq which exists in the P1-max.fasta file. I wonder how to solve this problem and 
how to keep all the seq in my MAP tree.

Best Regards and looking forward to your reply.

Yours Sincerely
Cynthia


((('Campylobacter':0.093559770846771,(('Methanothermobacter':0.040784570210273,
('Methanospirillum':0.053295205448348,(('Halorubrum':0.028862322005266,(('Cryptosporidium':0.027630861082570,
('Nosema':0.036746432083466,'Zea':0.020895144189279):0.011785671100725):0.013729189960639,
('Euglena':0.022469069740902,(('Drosophila':0.020414196489018,'Homo':0.010490034634827):0.004592406180122,
('Candida':0.070631464322680,('Caenorhabditis':0.009675663465433,
'Dictyostelium':0.044114901892989):0.015689239616266):0.012866036569656):0.007021999629922):0.014268162664734):0.048983715101415):
0.018671040910481,(('Thermoplasma':0.040657064314678,('Pyrobaculum':0.039486914796674,'Sulfolobus':0.047948994848777):
0.021537126842902):0.005813541443418,('Nanoarchaeum':0.044777898165511,('Methanococcus':0.042774812895935,'Thermococcus':
0.023086767892409):0.013912961019152):0.011871091665279):0.012410463832492):0.011293454863907):0.009038840619137):0.019451195838734,
('Bacillus':0.030512584692075,'Flavobacterium':0.036957501086869):0.007750716916581):0.008883532620250):0.011152163757441,
('Escherichia':0.035163495950644,('Thermotoga':0.050356239500052,'Thermus':0.011111262517438):0.017944074580493):0.007577767632376):
0.029784532489212)'Agrobacterium';

Benjamin Redelings

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Sep 30, 2019, 11:24:51 AM9/30/19
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Hi Cynthia,

I think the problem is that the root is placed on a leaf node.  I will try and fix this problem for the next version of bali-phy.

However, for now you can change the position of the root using the program `tree-reroot` that comes with bali-phy.  If the tree is in the file "my.tree", then you could write:

    tree-reroot my.tree --parent-of=Agrobacterium > my2.tree

This will create a copy of the tree in the file `my2.tree` where the root is moved to the parent node of Agrobacterium.

-BenRI

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