Why wont my newick file from MEGA open in FigTree?
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4.6 years ago
rdmitche ▴ 10

I produced a phylogenetic tree in MEGA X using the Max Likelihood method and get a nice looking tree. I want to transfer the tree file over to FigTree to change the layout, colors, etc. Note: this has worked in the past with no problem.

Now, when I use the command in MEGA that says "convert data to newick file" it does it, but when I try to open that file in FigTree I get the error "missing closing ')' in tree"

I'm thinking MEGA isn't converting the data to a Newick file proper, but how do I check this or fix it? I've messed around with add additional ")" all over the place with no luck.

Is there another tree viewer like FigTree that is just as easy to use that might work? Thank you.

software error phylogenetic tree MEGA FigTree • 6.8k views
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Can you post the tree file?

Newick is not a super well defined format, so usually if something like FigTree is complaining, its for good reason.

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You can try pasting the text of your tree file into an online viewer (e.g., ETE Toolkit), but as Joe said, there is probably an issue with the format of the file, you should view it in a text editor.

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Same exact issue here. I get this specifically when exporting trees with bootstrap values. E.g.:

(((((((((((Chet_BJ_EVM0006124,Chet_JL_Cor0014550.1)0.5400,Cav_TGdL_Haze_02754)0.7100,Cam_g3412)1.0000,(Cav_TGdL_Haze_07943,Chet_JL_Cor0163760.1)1.0000,(Osat_10g41130.1,(Osat_04g46440.1,Osat_02g43970.1)1.0000)0.5900,Osat_04g46400.1,Chet_JL_Cor0156810.1,((Chet_BJ_EVM0011762,Cav_Tom_Cav07g13740)1.0000,(((Chet_JL_Cor0193550.1,Cav_Tom_Cav11g13170)0.6800,Cav_TGdL_Haze_25802)1.0000,(Chet_JL_Cor0051550.1,(Cav_TGdL_Haze_21884,Cam_g24838)0.9100)1.0000)0.8200)0.9800)0.9800,((Cav_TGdL_Haze_08951,Cav_Tom_Cav03g18670)1.0000,((Chet_BJ_EVM0013717,Cman_G0007739)0.5200,Cam_g26066,(Cav_Tom_Cav09g01740,Cav_TGdL_Haze_19546)0.5000)1.0000)0.9100)1.0000,(Osat_01g73770.1,(((Cav_Tom_Cav10g05610,Chet_BJ_EVM0021922)0.6100,Cman_G0012172)1.0000,(Cav_Tom_Cav09g01950,Cman_G0007747,(Cav_TGdL_Haze_19557,Chet_BJ_EVM0020113)0.5600)1.0000)0.7900)0.5300)0.8000,((Osat_04g48350.1,Osat_02g45450.1)1.0000,(Osat_06g03670.1,Osat_09g35030.1)0.5900)0.9600)0.6900,(At_CBF3,(At_CBF1,At_CBF2)0.7900)1.0000)0.9400,((((Bpen_c2812,Bpen_c0079_dupelabel1)0.7700,Bpen_c0079)0.7400,(Bpen_c0075_dupelabel1,Bpen_c0075)0.8100)0.8100,(Cman_G0014289,(Cman_G0014293,Cman_G0014291)0.5700,(Cam_g17287,((Cav_Tom_Cav05g12880,Cav_TGdL_Haze_13764)0.6800,Cam_g17283)0.5400,(Chet_BJ_EVM0003046,Chet_JL_Cor0119160.1)0.9300,(Chet_JL_Cor0119170.1,Cam_g17285,Chet_BJ_EVM0011084,(Cav_Tom_Cav05g12910,Cav_Tom_Cav05g12900)0.6300)0.5800)0.5000)1.0000)0.9900)1.0000,((Bpen_c0278_dupelabel3,Bpen_c0278_dupelabel2)0.6500,(Bpen_c0278,Bpen_c0278_dupelabel1)1.0000)0.8800)0.9600,Cav_TGdL_Haze_08953,(Cman_G0022096,(Chet_BJ_EVM0013486,Cav_Tom_Cav03g18690,(Cav_Tom_Cav03g18700,Cam_g10982)0.6200)0.7700)0.9800((Cam_g10983,Cman_G0022097)0.5400,Chet_JL_Cor0080960.1,Cav_Tom_Cav03g18710)0.8500,(((Chet_BJ_EVM0008440,Cman_G0022095)0.5700,Chet_JL_Cor0080950.1)0.7100,Cam_g10981,(Cman_G0022094,((Cav_TGdL_Haze_08952,Cav_Tom_Cav03g18680)0.7600,(Cam_g10980,(Chet_BJ_EVM0017023,Chet_JL_Cor0080940.1)0.8000)0.6800)0.8200)0.9900)0.6200);

IcyTree tells me:

Expected token CLOSEP but found STRING (0.5400) at string position 1662.

Error context:
"... ,Cman_G0022097)0.5400,Chet_JL_ ... "

But I have no clue how to fix this....

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This is usually an unbalanced bracket issue. I could be wrong, but in my experience FigTree is usually expecting bootstraps/branch lengths to be preceded by a :.

I would try parsing the tree in to Biopython or ETE3 and writing it back out to see if they can fix it.

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