MCMCTree node numbers

[Alejandra Panzera]

Hello,

I am new to MCMCTree :) 

I am running an MCMCTree analysis with 188 loci (seq like) and 56 taxa. On the control file I am giving a soft bound for the age of the root and in the tree file I am giving calibration information for another two nodes. When I run the analysis I get this:

Fossil calibration information used.

Node  57:   B ( 0.1836, 0.3080, 0.0250, 0.0250 )

Node  60:   B ( 0.0550, 0.1474, 0.0250, 0.0250 )

Is there any way to get the tree with the node numbers ? I just want to verify that I have placed my soft bounds on the correct nodes. The tree is big so it is not very obvious.

Thank you all in advance for your help :) 

[Ziheng]

that info should be somewhere.  do you see on the screen something like the following:

************

Species tree

ns = 7  nnode = 13

 father   node  name                 time     sons          fossil

     11      1  human                0.00000

     12      2  chimpanzee           0.00000

     12      3  bonobo               0.00000

     10      4  gorilla              0.00000

     13      5  orangutan            0.00000

     13      6  sumatran             0.00000

      8      7  gibbon               0.00000

      0      8                       0.60001  ( 9  7)  U ( 1.0000, 0.0250 )

      8      9                       0.13509  (10 13)  B ( 0.1200, 0.1600, 0.0250, 0.0250 )

      9     10                       0.12197  (11  4)

     10     11                       0.08842  ( 1 12)  B ( 0.0600, 0.0800, 0.0250, 0.0250 )

     11     12                       0.01591  ( 2  3)

      9     13                       0.12021  ( 5  6)

((((1, (2, 3)), 4), (5, 6)), 7);

((((human, (chimpanzee, bonobo)), gorilla), (orangutan, sumatran)), gibbon);

((((human: 0.088419, (chimpanzee: 0.015913, bonobo: 0.015913): 0.072505): 0.033549, gorilla: 0.121967): 0.013120, (orangutan: 0.120206, sumatran: 0.120206): 0.014881): 0.464919, gibbon: 0.600006);

and in the main output file, there is somehting like this 

Species tree for FigTree.  Branch lengths = posterior mean times; 95% CIs = labels

((((1_human, (2_chimpanzee, 3_bonobo) 12 ) 11 , 4_gorilla) 10 , (5_orangutan, 6_sumatran) 13 ) 9 , 7_gibbon) 8 ;

you can run a very short chain to see the output, before running a long chain for the proper analysis.

ziheng

[Sishuo Wang]

Hi Alejandra,

I would recommend using treegraph or nw_display to visually examine it.

Sishuo

[Alejandra Panzera]

Thank you Ziheng and Sishuo for your help. I found now the easiest way for me to do this is to open the tree in FigTree, in node labels choose 'label' and if the tree is written correctly, it will display the calibration points. Thanks again!