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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 https://api.opentreeoflife.org/v3/tree_of_life/induced_subtree -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.

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 https://tree.opentreeoflife.org/opentree/opentree10.4@ott913935/Primates">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 https://tree.opentreeoflife.org/about/open-tree-of-life Studies that inform parts of the primate tree can be found in the "Supporting trees" panel for the relevant view of the tree at https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott913935/Primates if you want to cite the original publications.

Other reference: https://core.ac.uk/download/pdf/5103593.pdf

Members of Omorgus and Afromorgus are also currently divided among Pscoptera:Trogiidae and Coleoptera:Trogidae; all should be in Coleoptera:Trogidae https://en.wikipedia.org/wiki/Trogiidae https://en.wikipedia.org/wiki/Trogidae

Great! Feel free to add the tree in the curator so it can be included in the synthetic tree https://tree.opentreeoflife.org/curator Contact me if you have any questions!

I cannot make a GitHub account. When I try, it says the password has been compromised to athird party breach.

Sounds like you are trying to use a password on a list of known hacked passwords. Try creating your account with a different password:

https://blog.github.com/changelog/2018-07-31-new-improvements-and-best-practices-for-account-security-and-recoverability/

Thank you. I will try to add the tree now.

I added the study but I don't know how to add the tree. I mentioned this in the notes section but I searched for it later and couldn't find it. Hopefully someone else finds it and knows how to add the trees from the study.

I am sorry I couldn't add it. The good news is that people who know what they are doing can add the tree, I put the DOI url on the study somewhere. I can add it here, https://doi.org/10.1093/molbev/msu235

The title of the study is Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

I think I tagged it as Arachnida

Edit: paraphyletic

Hi Danielle, Thank you for your comments! Have you seen how to upload trees into the curator? More information is here: https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life 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! ejmctavish@ucmerced.edu

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

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).

and https://courses.lumenlearning.com/boundless-microbiology/chapter/archaeal-genetics/

I think you should take a look at this

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.

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 https://tree.opentreeoflife.org/taxonomy/browse?id=746703) not in Insectivora (see https://tree.opentreeoflife.org/taxonomy/browse?id=796664 ). 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".

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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515096/

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?

I tried to link to opentree.org because a website was required and it showed an error message

Here is the link I was trying to get to

https://tree.opentreeoflife.org/opentree/opentree9.1@ott155737/Lophotrochozoa

Hi Danielle, thanks for reporting the issue. Annelids are not flagged as extinct in our taxonomy. The taxonomy page for them is https://tree.opentreeoflife.org/taxonomy/browse?name=Annelida (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: https://tree.opentreeoflife.org/opentree/opentree9.1@mrcaott24ott102965/Myzostomida--Clitellata

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: https://github.com/OpenTreeOfLife/germinator/pull/112 and https://github.com/OpenTreeOfLife/reference-taxonomy/issues/238

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 https://github.com/OpenTreeOfLife/germinator/issues/85 ). 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.

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 https://gitter.im/OpenTreeOfLife/public 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: https://tree.opentreeoflife.org/contact

all the best, Mark

related: https://github.com/OpenTreeOfLife/reference-taxonomy/issues/160

Hi, Thanks for the comment. I agree that the age is an important thing to get right. I think you are referring to the tree that appeared https://www.scientificamerican.com/article/all-2-3-million-species-are-mapped-into-a-single-circle-of-life/ While that tree is based on work of this project, the age isn't. We are hoping to have age estimates for the nodes of the tree at some point, but currently our tree does not have age estimates.