I am exporting a phylogenetic tree with bootstrap from MEGA and I need the following NEXUS format to integrate the phylo data into a geometric morphometric analysis in MorphoJ software.
The following data is an example that can be imported into MorphoJ:
#NEXUS
BEGIN TREES;
Title Imported_trees;
LINK Taxa = Taxa;
TRANSLATE
1 fruticosa,
2 parvifolia,
3 palustris,
4 neumaniana,
5 crantzii,
6 pensylvani,
7 atro_Yellow,
8 atro_Gibson,
9 thurberi,
10 flabellifo,
11 aurea,
12 pimpinello,
13 argentea,
14 saundersia,
15 hirta,
16 heptaphyll,
17 thuringiac,
18 goldbachii,
19 recta,
20 dickinsii,
21 Rosa;
TREE 'Imported tree 0+' = ((((1,2),3),(((4,5),(((6,(7,8)),(9,10)),(((11,12),(((13,14),15),16)),((17,18),19)))),20)),21);
TREE 'Imported tree 1+' = (((((14,6),((16,(15,(((5,(13,4)),((7,8),(9,10))),((17,18),19)))),(11,12))),20),(3,(1,2))),21);
TREE 'Imported tree 2+' = ((((1,2),3),(20,(13,(((14,(7,8)),(10,9)),(((4,5),((17,18),19)),(((11,12),6),(15,16))))))),21);
TREE 'Imported tree 3+' = (((3,(1,2)),(20,(((14,6),(((13,(12,11)),((16,((7,8),((4,(17,18)),19))),15)),(5,10))),9))),21);
TREE 'Imported tree 4+' = ((((1,2),3),((9,(((10,5),((19,((((4,13),16),15),(17,18))),(12,((7,8),11)))),(14,6))),20)),21);
TREE 'Imported tree 5+' = (((3,(1,2)),(((12,11),((((((13,((5,4),((17,18),(15,16)))),19),(14,(7,8))),10),9),6)),20)),21);
TREE 'Imported tree 6+' = (((20,(((10,((14,(7,8)),6)),9),(((11,12),(15,(16,13))),(19,(4,(5,(17,18))))))),(3,(1,2))),21);
[etc.]
END;
Would I have to use a different software (e.g. Mesquite) to create such a format?
Many thanks,
Juniper
Hi Juniper,
From Mega, you can save your tree in newick format, which can then be read in programs such as FigTree that can export the tree(s) as a nexus file and including the tree annotations.
Best - Thierry
Thank you for your help Thierry, I have the newick files - I will give it a try in FigTree!
Many thanks,
Juniper
Dear Thierry,
And can you open Nexus tree files in MEGA?
Tried to convert the MrBayes output *.nex.con.tre to Newick format, and I could open that in MEGA. But unfortunately the Options/Branch/Display Statistics/Frequency is grayed out. And I would like to visualise the probability values too.
It is quite hand, that you can annotate subtrees in MEGA (clade name is displayed even if the clade is not collapsed); and also you can set an automatic limit for probability values, for instance, anything below 75% is not displayed. I really miss these features from FigTree.
Thx,
Gyozo
Hi Gyoso,
I guess you could open your tree.nex.con.tre in FigTree and then export it into Newick format to edit it in Mega.
Best - Thierry
Hi Gyozo,
Perhaps give it a try in Mesquite - I have been exporting/importing Newick trees from MEGA and they have been easy to edit.
Kind regards,
Juniper
Dear Juniper, Thierry,
I tried now both Mesquite and FigTree, but Geneious as well (latter one with and without support values). The export is always successful, MEGA opens the trees, but the Display Statistics/Frequency is always grayed out. It's a pity.
Anyway, thanks for your help!
Best regards,
Gyozo
Thierry really gave a good answer. Thank you for your help.
And I just describe it in more details.
Software: MEGA6.0; FigTree
Aim: Save your tree in newick format and import to FigTree to add further annotations.
Steps: In the Tree Explorter, click the "File" in the menu bar, then choose "Export Current Tree (Newick)".
Best regards,
Amy
i save my bootstrap tree in nwk format on mega and open it in figtree.. but the bootstrap value disappear. how to include it and make it appear in figtree?
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