The Newick format is an elegant format to describe phylogenetic trees but there are simpler formats (e.g., Rohlf, 1975, The Computer Journal and used in NTSYSpc) that are easier for humans to encode larger phylogenetic trees correctly. The Newick format was not as much of a problem back in 1986 when software usually dealt with much smaller trees. Perhaps someone should write a little conversion procedure for R.
F. James Rohlf Distinguished Professor, Emeritus and Research Professor Depts: Anthropology and Ecology & Evolution Stony Brook University On 4/12/2025 3:38:47 AM, Anneke van Heteren <[email protected]> wrote: Dear all, It turned out to be a superfluous bracket pair that made MorphoJ think there was a branch length missing. Many thanks to Chris for his help! Kind regards, Anneke Op za 12 apr 2025 om 14:33 schreef Anneke van Heteren <[email protected] [mailto:[email protected]]>: 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 [https://itol.embl.de/upload.cgi] accepts both and gives me trees that look correct. http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi [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 [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 [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 [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 <[email protected] [mailto:[email protected]]>: 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 [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 [email protected] [mailto:[email protected]]. To view this discussion visit https://groups.google.com/d/msgid/morphmet2/CAOZfLYoo0oUT0xQE-RLtbj6rchg7GQZVXYEtgejY9PcQr%2BD05Q%40mail.gmail.com [https://groups.google.com/d/msgid/morphmet2/CAOZfLYoo0oUT0xQE-RLtbj6rchg7GQZVXYEtgejY9PcQr%2BD05Q%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 [email protected]. To view this discussion visit https://groups.google.com/d/msgid/morphmet2/Mailbird-ec616cea-c678-44e2-a58c-9f93b08d3b46%40stonybrook.edu.
