Viewing a Lagrange tree


#1

I’m really new to all of this and learning as I go. I’m hoping a group like this will make all the difference, so I’m glad I found you! I am using Lagrange and am just wondering how to view the tree from the output file. I tried opening it in FigTree, but it only shows me the ML tree without any geographic range data.


#2

I have never used Lagrange. Most programs which add data to a treefile attach the data to the nodes or branches. Figtree has check boxes for whether or not to display node data and branch data if it exists. They are turned off by default.

I am not sure if you should post your treefile here, but maybe you could upload it to dropbox, figshare, or some other site and post a link to it here. If it is a reasonable size, not too huge, I see no reason not to just post it here so we could take a look and help you with it.


#3

Thank you! I truly appreciate any help. Here is a link to the output file of the demo: https://www.dropbox.com/s/8pl3wocbdypmkkb/psychotria_demo.results.txt

It’s a much smaller file than my own and should potentially work the same way and is giving me the same problem. While it does attach data to the nodes, the only thing I see is that it adds node numbers. Fig tree also splits it into five trees, although the first tree is the only one that is an actual tree.


#4

Notice this part of your text file

“Newick tree with interior nodes labeled: ((((((((P_hawaiiensis_WaikamoiL1:0.965685049879,P_mauiensis_Eke:0.965685049879)N2:0.708625793535,(P_fauriei2:1.23021851098,P_hathewayi_1:1.23021851098)N5:0.444092332438)N6:0.176711555244,(P_kaduana_PuuKukuiAS:1.85102239866,P_mauiensis_PepeAS:1.85102239866)N9:0.00088978628018)N10:0.334737598604,P_kaduana_HawaiiLoa:2.18575999726)N12:0.302349378005,(P_greenwelliae07:1.13136325525,P_greenwelliae907:1.13136325525)N15:1.35674612002)N16:1.68917027429,((((P_mariniana_MauiNui:1.99401105388,P_hawaiiensis_Makaopuhi:1.99401105388)N19:0.732827980356,P_mariniana_Oahu:2.72683903424)N21:0.257415170856,P_mariniana_Kokee2:2.9842542051)N23:0.460108485481,P_wawraeDL7428:3.44436269058)N25:0.732916958984)N26:0.734518574289,(P_grandiflora_Kal2:2.47930049109,P_hobdyi_Kuia:2.47930049109)N29:2.43249773276)N30:0.28731198987,((P_hexandra_K1:2.36398418918,P_hexandra_M:2.36398418918)N33:0.463044780206,P_hexandra_Oahu:2.82693999076)N35:2.37208124433)N36:0.0;”

Just copy everything (but the first phrase) in FigTree and Voilá! This parentical string is a tree in Newic format and the numbers inside are the values you calculated

hope It helps. Best!


#5

Thank you for replying to me. I am not sure that is the part of the data I am trying to get onto the tree. I think that this part may be what I’m looking for:

At node N36: split lnL Rel.Prob [K|KO] -35.93 0.487
[K|K] -36.22 0.3648
[K|O] -38.28 0.04659 [KO|K] -38.59 0.03422 [KO|O] -38.85 0.02622

At node N30: split lnL Rel.Prob [K|K] -35.31 0.9098
[KO|K] -37.98 0.06262

At node N26: split lnL Rel.Prob [K|K] -35.42 0.8129
[KO|K] -37.51 0.1
[O|KO] -39.39 0.01531 [K|KO] -39.45 0.01447 [KM|K] -39.51 0.01357

At node N16: split lnL Rel.Prob [O|K] -35.49 0.7563
[M|K] -37.32 0.121
[O|KO] -38 0.0613
[KO|K] -39.02 0.02209

At node N12: split lnL Rel.Prob [O|O] -35.55 0.7158
[OM|O] -36.74 0.2177
[O|KO] -39.07 0.02114

At node N10: split lnL Rel.Prob [OM|M] -35.26 0.9533

At node N6: split lnL Rel.Prob [M|O] -35.31 0.9066
[OM|O] -38.37 0.04261 [M|OM] -38.55 0.03558

At node N2: split lnL Rel.Prob [M|M] -35.23 0.982

At node N5: split lnL Rel.Prob [O|O] -35.24 0.9742

At node N9: split lnL Rel.Prob [M|M] -35.21 0.9991

At node N15: split lnL Rel.Prob [K|K] -35.23 0.977

At node N25: split lnL Rel.Prob [K|K] -35.44 0.7974
[KO|K] -37.75 0.07905 [KM|K] -38.15 0.05268 [KH|K] -38.21 0.05

At node N23: split lnL Rel.Prob [K|K] -36.27 0.3456
[O|K] -36.87 0.1895
[M|K] -37.1 0.1519
[H|K] -37.11 0.1498
[KO|K] -38.76 0.02883 [O|KO] -38.81 0.02729 [KM|K] -38.88 0.02554 [KH|K] -38.89 0.02518 [M|KM] -39.03 0.02187

At node N21: split lnL Rel.Prob [K|K] -37 0.1679
[O|O] -37.2 0.1367
[M|M] -37.26 0.1291
[H|H] -37.27 0.1272
[M|O] -37.89 0.06848 [H|O] -37.9 0.06798 [M|K] -37.98 0.06297 [H|K] -37.98 0.06271 [K|O] -37.98 0.06256 [MH|H] -39.85 0.009683 [MH|M] -39.85 0.009683 [M|OM] -39.93 0.008932 [H|OH] -39.94 0.008866 [O|KO] -40.02 0.008159 [K|KO] -40.02 0.008159 [KO|O] -40.12 0.007395 [OM|O] -40.15 0.00719

At node N19: split lnL Rel.Prob [M|H] -36.37 0.3153
[M|M] -37.37 0.1156
[H|H] -37.38 0.1146
[M|K] -37.77 0.07746 [K|H] -37.77 0.07741 [K|K] -38.22 0.04924 [M|O] -38.27 0.04686 [O|H] -38.27 0.04682 [O|O] -38.72 0.03006 [M|MH] -38.74 0.0293
[MH|H] -38.74 0.0293
[KM|M] -40.14 0.007198 [KM|K] -40.14 0.007198 [H|KH] -40.15 0.007194

At node N29: split lnL Rel.Prob [K|K] -35.23 0.9824

At node N35: split lnL Rel.Prob [K|O] -35.53 0.7261
[K|K] -37.39 0.1132
[K|KO] -37.53 0.09851 [KO|O] -38.33 0.04429

At node N33: split lnL Rel.Prob [K|K] -35.25 0.9638

I should get something resembling this:


#6

Here is a link to that same tree photo.


#7

In case anyone else comes across this problem, it turns out that RASP can run a Lagrange DEC analysis has it’s own tree viewer. It appears that my problem has been solved. Thanks for the input!