Dear Graham and Liam,

thanks for the quick responses; it works now! I knew I was missing
something trivial...

Best wishes,

Pedro

2018-05-14 12:52 GMT-03:00 Liam J. Revell <liam.rev...@umb.edu>:

> Dear Pedro.
>
> It looks like Graham has identified the problem - that the tree has some
> 'singleton' nodes. These are nodes with only one (rather than 2 or more)
> descendant edges. This can be fixed using:
>
> tree<-collapse.singles(tree)
>
> from the 'ape' package. Hopefully this helps.
>
> All the best, Liam
>
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> & Profesor Asociado, Programa de BiologĂ­a
> Universidad del Rosario
> web: http://faculty.umb.edu/liam.revell/
>
> On 5/14/2018 10:41 AM, Graham Slater wrote:
>
>> Hi Pedro,
>>
>> multi2di on this newick string returns a tree of 102 tips with 103 nodes,
>> so you seem to have a badly formatted tree. Plotting the resulting tree
>> with all edge lengths = 1 does not immediately reveal, at least to me,
>> where the issue(s) lie but perhaps it will to you?
>>
>> Graham
>> ------------------------------------------------------
>> Graham J. Slater
>> Assistant Professor
>> Department of the Geophysical Sciences
>> University of Chicago
>> 5734 S. Ellis Avenue
>> Chicago, IL 60637 USA
>>
>> Tel: (773) 702-0249
>> email: gsla...@uchicago.edu<mailto:gsla...@uchicago.edu>
>> www.fourdimensionalbiology.com<http://www.fourdimensionalbiology.com>
>>
>>
>>
>>
>>
>>
>> On May 14, 2018, at 10:16 AM, Pedro Pequeno <pacol...@gmail.com<mailto:
>> pacol...@gmail.com>> wrote:
>>
>> ((((((((((((Sp_102:16,Sp_101:16,Sp_100:16,Sp_99:16,Sp_98:16)
>> :5,(((Sp_97:13,Sp_96:13,Sp_95:13,Sp_94:13):4,Sp_93:17):2):2,
>> Sp_92:21):2,Sp_91:23):3,(Sp_90:24,Sp_89:24,Sp_88:24,Sp_87:
>> 24,Sp_86:24):2):10,((((((((Sp_85:2,Sp_84:2,Sp_83:2):10,Sp_
>> 82:12):10,Sp_81:23):2,(Sp_80:15,Sp_79:15):10):2,Sp_78:27):
>> 3,(((Sp_77:9,Sp_76:9):5,Sp_75:14,Sp_74:14):6,Sp_73:20):10):
>> 3,((Sp_72:22,Sp_71:22,Sp_70:22):5.5,Sp_69:28):5.5):3,((((
>> Sp_68:14,Sp_67:14):11,Sp_66:25,(Sp_65:12,Sp_64:12):12,Sp_63:
>> 25):7,(((((((Sp_62:4,Sp_61:4):4,Sp_60:8):4,Sp_59:12):2,((Sp_
>> 58:3.5,Sp_57:3.5):3.5,Sp_56:7):7):3,Sp_55:17):2,(Sp_54:15,
>> Sp_53:15):4):6,(Sp_52:20,Sp_51:20):5):7):2,((((Sp_50:17,
>> Sp_49:17):9,(Sp_48:20,Sp_47:20):6):2,(Sp_46:26,Sp_45:26):
>> 2):5,((Sp_44:20,Sp_43:20):10,((Sp_42:17,Sp_41:17,Sp_40:17,
>> Sp_39:17,Sp_38:17,Sp_37:17,Sp_36:17):12,(Sp_35:14,Sp_34:14):
>> 14):1):3):1):2):0.5):0.5,(Sp_33:29,Sp_32:29):8):8,((((((Sp_
>> 31:11,Sp_30:11):2,Sp_29:13):3,(Sp_28:8,Sp_27:8):8,((Sp_26:5.
>> 3,Sp_25:5.3):5.3,(Sp_24:5.3,Sp_23:5.3):5.3):5.3,Sp_!
>> 22:16,Sp_
>> 21:16):8):8,Sp_20:32):2,Sp_19:34):11):9,((((((Sp_18:14,Sp_17
>> :14):4,Sp_16:18):1,Sp_15:19):2,Sp_14:21):11,(Sp_13:21,Sp_12
>> :21,Sp_11:21):11):5,Sp_10:37):17):12,(((Sp_9:14,Sp_8:14,Sp_
>> 7:14):15,Sp_6:29):27,Sp_5:56):10):25,Sp_4:91):59,(Sp_3:62,
>> Sp_2:62):88):20,Sp_1:1.7e+02);
>>
>>
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>>
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