Hi Anneke! File B has too many opening brackets: 12 compering to close brackets: 11. I would say this is what couses your error. Regards Kamila
sob., 12 kwi 2025, 14:33 użytkownik Anneke van Heteren < a.h.vanhete...@gmail.com> napisał: > Dear all, > > special thanks to Donald and Miriam, who sent me suggestions off-list. > Unfortunately, nothing they said convinced MorphoJ either. > > I tried to compare an old newick string that I successfully imported in > MorphoJ in the past (A below) and the updated newick string I would like to > use now as part of a Nexus-file (B below). > https://itol.embl.de/upload.cgi accepts both and gives me trees that look > correct. http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi, however, > is only able to convert A into a Nexus-file. It gives an error for B: " > *Error:* Invalid Newick format!". I do not understand what is invalid > about B, since https://itol.embl.de/upload.cgi can read it without > problems. I tried asking a LLM to identify any syntax differences between > the two strings and it told me that the syntax per se (i.e., conforming to > the Newick format rules) is accurate for both. So, something is going on > with B that does not bother https://itol.embl.de/upload.cgi, and cannot > be identified, neither by me nor by LLM, but clearly is an issue for both > MorphoJ and http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi. > > If anybody has any ideas, I would be very grateful! > > All the best, > > Anneke > > > A: > (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3); > > B: > (Ame:21.8,((Tor:10.6,((Umi:0.0,((Uth:4.4,(Hma:3.6,Mur:3.6):0.8):0.6,(Uam:3.4,(Usp:1.2,((Uarf:0.0,Uar:0.4):0.5,Uma:0.9):0.3):2.2):1.6):0.0):5.6)):11.2); > > Op vr 11 apr 2025 om 19:34 schreef Anneke van Heteren < > a.h.vanhete...@gmail.com>: > >> Dear friends and colleagues, >> >> I am stuck on how to convince MorphoJ that it should weigh my phylogeny >> by branch lengths when applying "map onto phylogeny". I have pasted my >> phylogeny below for your information. As far as I can tell, all branches >> have a length and when I copy this phylogeny into >> https://itol.embl.de/upload.cgi, it looks exactly how I want it to be. >> Initially, I thought zero branch lengths might be the problem, but giving >> those an artificial length does not change anything; weighting by branch >> lengths remains greyed out/inactivated. >> I would very much appreciate any suggestions on how to fix this. >> Thanks in advance. >> >> Best wishes, >> >> Anneke >> >> >> (Ame:21.8,((Tor:10.6,((Umi:5.0,((Uth:4.4,(Hma:3.6,Mur:3.6):0.8):0.6,(Uam:3.4,(Usp:1.2,((Uarf:0.4,Uar:0.4):0.5,Uma:0.9):0.3):2.2):1.6):0.0):5.6)):11.2); >> > -- > You received this message because you are subscribed to the Google Groups > "Morphmet" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet2+unsubscr...@googlegroups.com. > To view this discussion visit > https://groups.google.com/d/msgid/morphmet2/CAOZfLYrp%2BHFA6bgk91eN6neY_BXwwNmbkdmT2gvdDPoDNiVJUg%40mail.gmail.com > <https://groups.google.com/d/msgid/morphmet2/CAOZfLYrp%2BHFA6bgk91eN6neY_BXwwNmbkdmT2gvdDPoDNiVJUg%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet2+unsubscr...@googlegroups.com. To view this discussion visit https://groups.google.com/d/msgid/morphmet2/CAPgkZKrePCi2LH5Sp7i_OO0h3LPoUjeXYCGbPxS7h-dRVj-FNg%40mail.gmail.com.
