Dear all,
I am trying to create a consensus skyline plot using the "ape"
package(newbie).
I have a nexus file that looks like the one from above containing many
trees. (my_file.trees)
#NEXUS
begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)]
tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0,
(20.1:1, 4.1:0):0):1, ((37.1:0, (23.1:0, 29.1:0):0):0, 15.1:0):3):7,
(36.1:3, (40.1:0, 26.1:1):2):1):2, ((16.1:0, 33.1:0):3, (10.1:0,
18.1:0):2):8):46, ((((6.1:1, (11.1:0, 34.1:0):0):2, 2.1:1):19, (((38.1:4,
(35.1:4, ((8.1:0, 42.1:0):1, 22.1:0):3):2):0, ((5.1:2, (27.1:0,
39.1:0):0):0, (17.1:0, 30.1:0):1):4):8, ((31.1:0, ((41.1:0, (7.1:0,
25.1:1):0):0, 3.1:0):3):0, (12.1:0, (14.1:0, 1.1:0):0):0):13):10):14,
(((24.1:0, 9.1:0):0, 32.1:0):1, 19.1:0):25):20):206);
tree true_tree_2 = [&U] ((((37.1:4, ((36.1:0, 25.1:0):0, 39.1:0):2):0,
33.1:1):2, (1.1:0, 43.1:0):1):81, (((((21.1:1, (38.1:1, 14.1:1):0):3,
(((29.1:0, 35.1:0):1, 4.1:1):1, ((41.1:1, (24.1:0, ((8.1:0, 32.1:0):0,
7.1:0):0):1):0, (10.1:2, (6.1:1, (26.1:1, (15.1:0,
16.1:0):0):0):0):2):0):4):1, (28.1:1, (3.1:1, 13.1:0):0):7):12, (((22.1:5,
(((2.1:1, 34.1:1):0, 19.1:0):3, (18.1:0, 42.1:0):3):0):0, 17.1:0):3,
(27.1:14, (((30.1:0, 23.1:0):1, 31.1:0):1, 5.1:2):5):3):5):9, ((11.1:0,
9.1:1):0, (12.1:0, (20.1:0, 40.1:1):1):3):23):67);
I haven't managed to read this file content using the *read.tree* function
..
Error in if (tp[3] != "") obj$node.label <- tp[3] :
missing value where TRUE/FALSE needed
Does anyone know first of all, why I cannot read this file (not even with
read.nexus function)? And secondly how can one generate an "average" skyline
plot from several trees?
Thank you in advance!
Cheers!
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