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  • Newick tree downloaded via API does not open in any tree viewing software on GitHub

    First: We published our paper where we use and cite the OTOL ( a few months back. So thank you for this tool. We are at it again and now I am trying to download an induced tree for visualization, but the newick format does not open in any tree visualization software that I have tried so far (figtree, TreeViewX). This happens with both larger (20) and smaller (5) taxons in the POSt data. The command is: curl -X POST -H "content-type:application/json" -d '{"ott_ids":[770315, 542509, 505714, 395048, 316451, 153563, 940184, 1005914, 550662, 773491, 3644159, 395686, 801608, 1096512, 13567, 1083289, 110468, 5132284, 812825]}' > tree.newick Please let me know of any software that I can run on Linux (Mac would also work) that opens these newick files... I will try to find a work-around by myself, but it would be nice if this worked out of the box!

    • Hi, thanks for the report. I'll look into adding a "simplified" newick option to the web-service call. I think the problems usually arise from 2 aspects of our tree that are not common:

      1. we have labels that contain open- and closed- parentheses. We quote them properly, but not all software is happy with them. Originally we had some of these because of tip names that we imported in out taxonomy from other sources. Now some are being added my our homonym-disambiguation steps in production of the taxonomy.
      2. we emit nodes with out-degree = 1. Many tree reading tools don't like that.

      I did check that newick string from your call, and I think it is valid. There are other contexts in which suppress the difficult name and "monotypic" nodes. I'll see how easy it would be to add those features to the web-service call. I'll leave this issue open until I have time to check and report back.

    • I was able to open the tree in treeviewx. Running tv tree.newick didn't work, but running tv and then selecting the file from the menu did work.

      Note that the curl command doesn't return newick format. Instead, it retrieves a JSON file with the newick string embedded in it. One way to extract the newick using the command line is to install the tool jq and run: curl -X POST -H "content-type:application/json" -d '{"ott_ids":[770315, 542509, 505714, 395048, 316451, 153563, 940184, 1005914, 550662, 773491, 3644159, 395686, 801608, 1096512, 13567, 1083289, 110468, 5132284, 812825]}' | jq -r .newick > tree.newick

      It looks like figtree hangs if the number of degree-1 nodes is too high. Perhaps the drawing time is exponential in the number of degree-1 nodes.

  • I found a study on echinoderm phylogeny supporting Asterozoaon GitHub

    I found a study supporting Asterozoa for Echonodermata Will add tree soon

    • Download in Newick format dysfunctional on GitHub

      Starting from a few weeks ago, I cannot download a subtree anymore in Newick format. There seems to have been also some change with the download URL recently. I need to download regularly the vertebrate subtree ( and luckily I have an old version of the tree, which works for my script, but it will become outdated with time :-(

      • hmm that is odd that it changed a few weeks ago. we did change some of the back-end software on Monday. I'll try to figure out what is going on. There is a limit on the number of tips that can be downloaded from the web services. But if you have the entire vertebrate tree via a previous download, that seems like a poor explanation...

      • and thanks for the bug report!

      • Still gives my nothing when I try to download the vertebrate subtree in newick format :-( Maybe you have changed the limits? I manage with smaller subtrees, but e.g. also the amniota phylum fails. The downlaoded filecontains only the string "NEWICKNOTFOUND"

      • Confirmed, this tree won't load, while I'm able to fetch the">primate tree as Newick successfully. Could be a problem with larger clades, or perhaps a "poison pill" (funky Unicode taxon name)?

      • It's working again, thanks. If I reference this tree in a scientific publication, how should I cite it?

      • Great. General guidelines for citation of parts of the project are at Studies that inform parts of the primate tree can be found in the "Supporting trees" panel for the relevant view of the tree at if you want to cite the original publications.

    • Incorrect synonymy (Orchamoplatus)on GitHub

      The taxonomic name reconciliation service considers Orchamoplatus to be a synonym of Orchamus. Since Orchamoplatus is a genus of Hemiptera, and Orchamus is Orthoptera, this is likely incorrect. A google search did not turn up any evidence that there was even an Orchamoplatus genus in the orthoptera, although Hemiptera:Orchamoplatus was originally called Hemiptera:Orchamus, so possibly that is the source of confusion?

    • Incorrect synonymy (Delia vs Dellia)on GitHub

      The taxonomic name reconciliation service considers Diptera:Neohylemyia monticola a synonym of Orthoptera:Dellia monticola. It should probably be a synonym of Diptera: Delia monticola.

      • Trox in Insecta:Psocoptera:Trogiidae, should be in Insecta:Coleoptera:Trogidaeon GitHub

        The members of the beetle family Trox are found in two places: Insecta:Psocoptera:Trogiidae and Insecta:Coleoptera:Trogidae.

        As far as I can tell, there is not genus Trox in the Trogiidae, so all members of that genus are beetles and should be in Trogidae.

      • Phylogeny of chelicerata.on GitHub

        This study new phylogenic tree with 10p% bootstrap suplort

      • Ameobozoan relationships molecular analysison GitHub

        I found a study that should shed more light on ameobozoan relationships.

        • Study showing possible eukaryotes treeon GitHub

          I am searching for molecular studies to attempt to resolve eukaryotes phylogeny. The more phylogenies that are incorporated, the more data we can incorporate into the synthetic tree, hopefully resulting in more accuracy.

          • Study shows sponges diverged first. LBA is implicated to be why Ctenophores showed up as basalon GitHub
            • Cepaea genus (Gastropoda, Helicidae) polyphylyon GitHub

              I fond a study revealing that Cepaea is polyphyletic

              • Mollusca Infoon GitHub

                This link brings you to a page detailing the various hypotheses as to how the various mollusca Claude’s are related. Please give it a read.

                • Vascular Plant phylogenyon GitHub

                  Here is a phylogenies tree of vascular plants. It’s good to have more data. I am not correcting anything, just showing a phylogeny that, if not already incorporated, could be incorporated.

                  • Unikont/bikont now into questionon GitHub

                    I found a study finding Escavates at the root and SARP and AMR being the next brannches

                    • New study I found about systematic errors in molecular phylogenies and how people minimize those errorson GitHub
                      • Here is a study comparing similarities and differences in possible Molluca phylogenyon GitHub

                        I was curious about Mollusca phylogeny and found a study i will link to which gathered various morphological and molecular trees to determine the many differences that exist in phylogenic trees of Mollusca


                        • Careful with understudied phyla: The case of chaetognathon GitHub

                          I found a study about Chaetognath that places them as the sister group to the rest of Prodtostomes

                          • Monoplacophora is polyphyleticon GitHub

                            perhaps it would be a good idea to make the tree monophyletic

                            • Edit: paraphyletic

                            • Hi Danielle, Thank you for your comments! Have you seen how to upload trees into the curator? More information is here: It is the best way to update the relationships in the tree. Contact me if you want any information or help on how to do that!

                            • I added a chelicerata study to the database but I don't know how to add trees, and I tried searching for the study and had trouble finding it

                            • I added a chelicerata study to the database but I don't know how to add trees, and I tried searching for the study and had trouble finding it

                          • Pancrustacea studyon GitHub

                            I've been searching for info about isopods and found this study

                            • Pelmatozoa no longer a cladeon GitHub

                              Pelmatozoa is no longer a clade. The members do not share common ancestry

                              • Servers down?on GitHub

                                Hello, I am currently unable to access your webpage or download anything through R. Just wondering if the server is down or any other issue? Have double checked this with multiple devices. Thanks, Mike

                                • Thanks for reporting this. The server is being very slow for me too. I'll try to diagnose the issue. I can ssh into the front-end and the back-end. But something is definitely not working as intended...

                                • seems to be more responsive now. I did try to restart apache, but it is acting more like a general network latency problem with wherever the server sits (as opposed to something that I fixed).

                              • Eukaryota and Archea more closely related to each other than to bacteriaon GitHub

                                I’ve been reading about how Archaea and Eukaryota might be closely related to each other more than to bacteria

                              • Dotted lines?on GitHub

                                What do the dotted lines mean? What do the solid lines mean?

                                • If you click on the grey oval with the word "Legend" above the tree, the page should show you a key to the visual elements used on the page. Branches that are placed entirely based on the taxonomy are dashed. The solid edges have some support from at least one published phylogenetic tree.

                              • Insectivora Wastebasket Taxonon GitHub

                                I remember reading in different places that Insectivora was a wastebasket taxon and the animals in that section were moved to different categories. Unfortunately I don't remember where I read that from. Is it possible to update the synthetic tree so Insectivora is removed and the families relocated?

                                • Agreed. I think this has been discussed before. (Previously reported as #375.) But we can’t include any information without some kind of reference. Any chance you could find us a good modern taxonomic treatment in this area? NCBI claims that its Insectivora has Soricomorpha as a synonym (the name that CoL uses). It’s possible that NCBI has redefined the name to fit some improved hypothesis of monophyly. But it's also possible neither NCBI and CoL is up to date.

                                  Understanding the situation is more work than I can do now, so any help would be welcome.

                                • note that we have the Afrotherian mammals with common names including "shrews" and "moles" in Afrotheria (see not in Insectivora (see ). So the most egregious cases of Insectivora being a wastebasket are correctly dealt with. There may be some issues remaining, but I'm not aware of them.

                                  There is the question of whether we should call the group "Insectivora" or "Eulipotyphla." I personally wouldn't mind using Eulipotyphla, because it conveys the fact that we aren't using the "old" definition of Insectivora. But NCBI uses Insectivora, so that is was is used in OTT. I don't really mind using "Insectivora".

                              • Species Concept?on GitHub

                                Which species concept is used in the synthetic tree for which groups?

                                • Hi, The Open Tree project does not do any alpha taxonomy, so I think that it is hard to think of it as having any specific species concept implemented. We use a taxonomy that is assembled programmatically from other taxonomy inputs (and corrections from users). If you'd like more details on that process see

                                  As a result, the species concepts used by many authors get incorporated (via the input taxonomies), and I am confident that their is a lot of internal inconsistency about what species concept is used as you browse across the open tree.

                                • Is there a way to add something in the properties area that tells which species concept is used in each study in the Details section?

                                • Not for any feasible level of programming effort.

                                  I doubt there is a simple enumeration of species concepts. The intended design is that if someone cares that much about the details of a species definition, they would trace references, first to the source taxonomy and then to the sources it uses. Unfortunately few of the source taxonomies will tell you which 'taxon concept' (i.e. published description) applies to their use of a name, because a name (even when the authority is known) often gets reused for many difference 'taxon concepts', each perhaps with its own 'species concept', without any indication of the fact - an endemic horror in taxonomy. And then there is the issue that phylogenetic tree curation is not so carefully done that we're always sure a given sample belongs is assigned correctly to an OTT taxon (with its particular 'taxon concept'), even if the names match exactly.

                                  What is your use case, out of curiosity?

                              • Annelidaon GitHub

                                I notice on the.synthetic tree annelids are not on there and when I.look for them on the database it thinks they are extinct

                                • I tried to link to because a website was required and it showed an error message

                                • Hi Danielle, thanks for reporting the issue. Annelids are not flagged as extinct in our taxonomy. The taxonomy page for them is (I do realize that the "e.g. extinct" text at the top of the page may make it look like they are flagged that way, but that is intended as explanatory note to show what the flags look like.

                                  I think you can find most of them from navigating around:

                                  I think that they don't show up in the tree because the current tree does not put Myzostomida with the rest of the Annelids. Taxonomies vary on what goes inside Annelida. If you are curious about the details, there are a couple of Open Tree GitHub issues where this is discussed: and

                                  The longer term solution is for the browser to show you the relevant part of the tree when a taxon is not monophyletic. This has been a long standing issue (see ). The good news is that we are pretty close to having a new tool for serving up the synthetic tree that would fix this. Unfortunately, it still needs a bit more testing before being deployed.

                                • Thank you. I didn't know Annelida wasn't monophyletic. Thank you for teaching me. I think a Tree of Life should consist of monophyletic lineages and try and stay away from paraphyletic and polyphyletic lineages. I am not a professional taxonomist I just like to research this kind of thing. It's interesting to me.

                                • Myzostomida is a genetic outlier and gets put in different places by different studies. I think Annelida could only be seen as nonmonophyletic if you believed both that Myzostomida is outside of it taxonomically (as NCBI says) and that Myzostomida is deep enough inside of it phylogenetically. Both of these claims are pretty weak, so don't call it quits yet.

                              • Is this project still active?on GitHub

                                I'm interested in this area and I am trying to determine if this project is still active. The latest links to the Blog area yield results which don't have a date and the last dated entry is for spring of 2016. If this effort is still being conducted, how do I find information about the project and what is currently being done?

                                • Hi Philip, yes the project is still active (though not as many people are working on it as last year). We are seeking more funding and hope to continue to support it for years to come.

                                  The software developers use an open chat at to discuss issues. So that is probably the best place for a short query, but using the email list is also fine. The lists are described at:

                                  all the best, Mark

                              • Allow the search for known familiar animalson GitHub

                                Like chicken, dog, horse, etc.

                              • New synthesis for Thecostraca?on GitHub

                                I realized that I had left some trees unrooted in the tree collection for barnacles. I fixed this issue, and would really like to know if it improved the synthesis tree. As of now, the placement of some taxa is incorrect, e.g. Tetraclita and Tetraclitella should be close relatives, but Tetraclita has been removed from the synthesis. Any chance you can re-run the synthesis, at least for the Thecostraca? Sorry I didnt catch this earlier, I only saw it when I started using the tree in depth.

                                Thank you, Christine

                                • Is Life only 3.5 billion years old, or older?on GitHub

                                  The latest research shows life may be 3.8, or even 4.1 billion years old, not 3.5 as shown in the Circle of Life. See here: This matters greatly since the earlier life began on Earth, the easier it presumably is to establish. This has profound effects on our expectations for life on other worlds too, as we ramp up our collection of Earth-like planets in the galaxy and beyond. Please consider updating the origin of life date in your model.