Dear look your data the "tree.phy" Inside BEGIN TAXA; the name of tax need be exactly equals in as TRANSLATE see my .phy example bellow the same error are occurring to me (the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis.) I solve it by change the taxon macularius, this taxon was with an extra h at the end in the section TRANSLATE. a just remove this "h" and tried to run the command again, and no error/warning message.
#NEXUS BEGIN TAXA; DIMENSIONS ntax=5 TAXLABELS macularius pusilla collaris semipalmatus antilarum ; END; BEGIN TREES; TRANSLATE 1 maculariush, 2 pusilla, 3 collaris, 4 semipalmatus, 5 antilarum, ; TREE tree_1 = [&R] ((1:0.10820559,2:0.07532207):0.04591014,(3:0.55047517,4:0.01800012):0.07815226,5:0.07346231); END; -- Patrick Douglas Corrêa Pereira Laboratório de Biologia Molecular e Neuroecologia - Instituto Federal do Pará Campus Bragança. Rua da Escola Agrícola s/n, Vila Sinhá, Bragança, Pará, Brasil. Telefone: +55 (91) 9 85404339 E-mail: patrickpereira...@gmail.com patr...@ufpa.br patrickpereira...@hotmail.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/