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davidemms / STAG

STAG: Species Tree from All Genes
GNU General Public License v3.0
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support values #3

Closed hui-liu closed 4 years ago

hui-liu commented 4 years ago

Hi,

I used stag to infer the species tree using gene trees. I got a species tree file SpeciesTree.tre. I think the numbers in the tree is the branch lengths. I also would like to display the support value for each branch but I failed to found it. Could you please where can I find it? Thank you very much.

davidemms commented 4 years ago

Hi

The tree is in Newick format and the support values are in the SpeciesTree.tre file, you can confirm this by opening the file in a text editor. The table here gives a good overview of the newick format: http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees. How you display the values will depend on what you are using to view the tree, but they will usually be displayed by default by most tree viewers e.g.: http://etetoolkit.org/treeview/

All the best David

hui-liu commented 4 years ago

Thank you!

I checked the SpeciesTree.tre file again. I found 3 trees in the file. For example, is the support value for Malus_domestica and Betula_pendula the 0.115517 in the first tree? I think there are only branch lengths in the second one and the third one. If I am not correct please tell me. Thank you. And, Could I know what is the difference between these two trees? I only noted that a prefix b in the 2nd one.

Best regards, Hui Liu

(Eucalyptus_grandis:0.0840676,(((Malus_domestica:0.180349,Betula_pendula:0.0555429)0.115517:0.0279742,(Cucumis_sativus_L.:0.0955262,Medicago_truncatula:0.101965)0.0862069:0.0247052)0.0310345:0.0212108,((((Malania_oleifera:0.0957311,Vitis_vinifera:0.0606077)0.156897:0.0264332,(Aquilegia_coerulea:0.0944895,((((Physcomitrella_patens:0.430799,((((Picea_abies:0.0294748,(Pinus_taeda:0.0673564,Pinus_lambertiana:0.00140267)0.593103:0.0441746)0.405172:0.0322985,Pseudotsuga_menziesii:0.0341528)0.806897:0.0740524,Ginkgo_biloba:0.0903614)0.414655:0.0551971,Gnetum_montanum:0.197425)0.553448:0.0690962)0.816379:0.111652,Amborella_trichopoda:0.130519)0.459483:0.0558678,Zostera_marina:0.22893)0.231897:0.0394231,Cinnamomum_kanehirae:0.0889986)0.296552:0.0421389)0.340517:0.0380863)0.0353448:0.014932,(((Nicotiana_tabacum:0.0918885,(Mimulus_guttatus:0.0677004,Handroanthus_impetiginosus:0.0544367)0.765517:0.0542202)0.368103:0.0318588,Artemisia_annua:0.122846)0.203448:0.0274722,Camellia_sinensis:0.075083)0.142241:0.0268814)0.025:0.0171124,(Beta_vulgaris:0.127856,Arabidopsis_thaliana:0.143442)0.111207:0.0338897)0.0189655:0.0155223)0.0232759:0.0134723,(Xanthoceras_sorbifolium:0.0636795,(Salix_purpurea:0.0169842,(((Populus_tremuloides:-0.000133792,(Populus_tremula_X_tremuloides:-0.000417674,Populus_tremula:0.000356001)0.381034:0.00409638)0.598276:0.00576762,Populus_trichocarpa:-0.000518475)0.303448:0.00421787,Populus_euphratica:0.00264967)0.650862:0.0113229)0.906897:0.0580104)0.140517:0.0202371);
b((((((Picea_abies:0.029474800000000023,(Pinus_taeda:0.06735639999999998,Pinus_lambertiana:0.0014026700000000503):0.04417459999999995):0.03229850000000001,Pseudotsuga_menziesii:0.03415279999999998):0.07405239999999996,Ginkgo_biloba:0.09036139999999998):0.0551971,Gnetum_montanum:0.19742500000000002):0.0690962,(Amborella_trichopoda:0.13051899999999994,(Zostera_marina:0.22892999999999997,(Cinnamomum_kanehirae:0.08899860000000004,(Aquilegia_coerulea:0.0944895,((Malania_oleifera:0.09573109999999996,Vitis_vinifera:0.06060769999999993):0.026433200000000046,((((Nicotiana_tabacum:0.09188850000000004,(Mimulus_guttatus:0.0677004,Handroanthus_impetiginosus:0.054436700000000005):0.05422020000000005):0.031858799999999965,Artemisia_annua:0.12284600000000001):0.027472200000000058,Camellia_sinensis:0.07508300000000001):0.026881399999999944,((Beta_vulgaris:0.12785599999999997,Arabidopsis_thaliana:0.14344199999999996):0.03388970000000002,(((Malus_domestica:0.18034899999999998,Betula_pendula:0.05554289999999995):0.02797420000000006,('Cucumis_sativus_L.':0.09552620000000012,Medicago_truncatula:0.10196500000000008):0.024705199999999983):0.021210799999999974,(Eucalyptus_grandis:0.08406760000000002,(Xanthoceras_sorbifolium:0.0636795,(Salix_purpurea:0.016984200000000005,(((Populus_tremuloides:0.0,(Populus_tremula_X_tremuloides:0.0,Populus_tremula:3.560009999999947E-4):0.004096380000000011):0.005767619999999973,Populus_trichocarpa:0.0):0.004217870000000068,Populus_euphratica:0.0026496700000000484):0.011322899999999914):0.05801040000000002):0.020237100000000008):0.013472299999999993):0.015522299999999989):0.017112400000000028):0.014931999999999945):0.03808630000000002):0.04213889999999998):0.039423100000000044):0.05586780000000002):0.11165199999999997):0.2153995,Physcomitrella_patens:0.21539949999999994);
((((((Picea_abies:0.029474800000000023,(Pinus_taeda:0.06735639999999998,Pinus_lambertiana:0.0014026700000000503):0.04417459999999995):0.03229850000000001,Pseudotsuga_menziesii:0.03415279999999998):0.07405239999999996,Ginkgo_biloba:0.09036139999999998):0.0551971,Gnetum_montanum:0.19742500000000002):0.0690962,(Amborella_trichopoda:0.13051899999999994,(Zostera_marina:0.22892999999999997,(Cinnamomum_kanehirae:0.08899860000000004,(Aquilegia_coerulea:0.0944895,((Malania_oleifera:0.09573109999999996,Vitis_vinifera:0.06060769999999993):0.026433200000000046,((((Nicotiana_tabacum:0.09188850000000004,(Mimulus_guttatus:0.0677004,Handroanthus_impetiginosus:0.054436700000000005):0.05422020000000005):0.031858799999999965,Artemisia_annua:0.12284600000000001):0.027472200000000058,Camellia_sinensis:0.07508300000000001):0.026881399999999944,((Beta_vulgaris:0.12785599999999997,Arabidopsis_thaliana:0.14344199999999996):0.03388970000000002,(((Malus_domestica:0.18034899999999998,Betula_pendula:0.05554289999999995):0.02797420000000006,('Cucumis_sativus_L.':0.09552620000000012,Medicago_truncatula:0.10196500000000008):0.024705199999999983):0.021210799999999974,(Eucalyptus_grandis:0.08406760000000002,(Xanthoceras_sorbifolium:0.0636795,(Salix_purpurea:0.016984200000000005,(((Populus_tremuloides:0.0,(Populus_tremula_X_tremuloides:0.0,Populus_tremula:3.560009999999947E-4):0.004096380000000011):0.005767619999999973,Populus_trichocarpa:0.0):0.004217870000000068,Populus_euphratica:0.0026496700000000484):0.011322899999999914):0.05801040000000002):0.020237100000000008):0.013472299999999993):0.015522299999999989):0.017112400000000028):0.014931999999999945):0.03808630000000002):0.04213889999999998):0.039423100000000044):0.05586780000000002):0.11165199999999997):0.2153995,Physcomitrella_patens:0.21539949999999994);
davidemms commented 4 years ago

Hi Hui Liu

Are you sure there are 3 trees in the results file, "SpeciesTree.tre"? There should only be one tree. Once you've confirmed this, could you please let me know the complete set of steps to reproduce this behaviour so I can investigate it.

All the best David

hui-liu commented 4 years ago

Hi David,

I found the SpeciesTree.tre file I previous checked was a copy version from figfree. I saved the tree generated from stag, and then I got 3 trees in one tree file. I don't know why this happened.

I am so sorry about that.

Best regards, Hui Liu