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Open Tree of Life

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This is the mailing list for Open Tree of Life (http://opentreeoflife.org), an NSF-funded project to build an evolutionary tree for all species and the framework to continually edit and revise the draft tree.

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Christine Ewers, Sandro Ceccone2

Apr 14

Choosing specific ("best") backbone phylogeny?

Good morning everyone, I'm new to this chat and I'm not a phylogenetic biologist, so I

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Choosing specific ("best") backbone phylogeny?

Good morning everyone, I'm new to this chat and I'm not a phylogenetic biologist, so I

Apr 14

monica steffi matchado, Karen Cranston2

7/16/20

Supporting files for QIIME2

Hi Monica, I just replied over on the open github issue: https://github.com/OpenTreeOfLife/opentree/

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Supporting files for QIIME2

Hi Monica, I just replied over on the open github issue: https://github.com/OpenTreeOfLife/opentree/

7/16/20

Mark Holder, Emily Jane McTavish2

4/20/20

Link to Info page for updates on the April 11 hack that has caused Open Tree downtime

Hi all, The Open Tree of Life websites and API are back online! We have temporarily paused study

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Link to Info page for updates on the April 11 hack that has caused Open Tree downtime

Hi all, The Open Tree of Life websites and API are back online! We have temporarily paused study

4/20/20

4/11/20

Open Tree of Life update on April downtime

Hello, Today (Apr 11 in the afternoon US time) several of the Open Tree of Life web-servers were

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Open Tree of Life update on April downtime

Hello, Today (Apr 11 in the afternoon US time) several of the Open Tree of Life web-servers were

4/11/20

Cody Hinchliff, … Hilmar Lapp7

11/21/18

Fwd: Permission of a paper's figure

The only problem that I can see here is the question on what you actually have the copyright on. Is

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Fwd: Permission of a paper's figure

The only problem that I can see here is the question on what you actually have the copyright on. Is

11/21/18

7/26/18

possible downtime Thursday, July 26 and Friday, July 27 201

Hi folks, Sorry the dates were wrong in the previous email... Due to some maintenance tasks by our

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possible downtime Thursday, July 26 and Friday, July 27 201

Hi folks, Sorry the dates were wrong in the previous email... Due to some maintenance tasks by our

7/26/18

7/26/18

possible downtime Thursday, July 20 and Friday, July 21 2018

Hi folks, Due to some maintenance tasks by our cloud-computing provider, the servers for our front-

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possible downtime Thursday, July 20 and Friday, July 21 2018

Hi folks, Due to some maintenance tasks by our cloud-computing provider, the servers for our front-

7/26/18

Alexander Ulrich, … Joseph Brown15

1/23/17

How can I obtain a phylogenetic tree for a subset of species?

Hi Joseph, Thank you so much for your help and effort! I think you are right, since ~ 1/3 can not be

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How can I obtain a phylogenetic tree for a subset of species?

Hi Joseph, Thank you so much for your help and effort! I think you are right, since ~ 1/3 can not be

1/23/17

12/7/16

OpenTree v 8.0 and easier addition to synthesis

We have a new version of the synthetic tree and an easier way to add trees to synthesis. == New

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OpenTree v 8.0 and easier addition to synthesis

We have a new version of the synthetic tree and an easier way to add trees to synthesis. == New

12/7/16

9/23/16

new versions of tree and taxonomy

We have just release version 7.0 of Open Tree of Life, along with version 2.10 of the Open Tree

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new versions of tree and taxonomy

We have just release version 7.0 of Open Tree of Life, along with version 2.10 of the Open Tree

9/23/16

8/5/16

new synthesis tree; other features

We have just released a new version of the synthetic tree as well as some new website features: I.

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new synthesis tree; other features

We have just released a new version of the synthetic tree as well as some new website features: I.

8/5/16

Yan Wong, … Tony Rees5

7/5/16

Change in new version of IRMNG as of now (Uncia uncia -> Panthera uncia), thanks... Tony Rees, New

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Change in new version of IRMNG as of now (Uncia uncia -> Panthera uncia), thanks... Tony Rees, New

7/5/16

Marc Jones, … Jonathan A Rees4

7/4/16

Rhynchocephalia

Fixed in draft taxonomy (not yet on web site). Tracking at https://github.com/OpenTreeOfLife/feedback

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Rhynchocephalia

Fixed in draft taxonomy (not yet on web site). Tracking at https://github.com/OpenTreeOfLife/feedback

7/4/16

5/10/16

returning references with subtrees

A long outstanding OpenTree issue has been the need to return a reference list along with any subtree

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returning references with subtrees

A long outstanding OpenTree issue has been the need to return a reference list along with any subtree

5/10/16

Karen Cranston, … Yan Wong20

4/19/16

new versions synthesis tree, APIs

On 19 Apr 2016, at 21:21, Mark Holder <mtho...@gmail.com> wrote: > sorry for the delay. No

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new versions synthesis tree, APIs

On 19 Apr 2016, at 21:21, Mark Holder <mtho...@gmail.com> wrote: > sorry for the delay. No

4/19/16

Christine Ewers, … Mark Holder17

4/13/16

New synthetic tree for barnacles collection?

Hi, Thanks for pointing this out. I started an issue https://github.com/OpenTreeOfLife/reference-

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New synthetic tree for barnacles collection?

Hi, Thanks for pointing this out. I started an issue https://github.com/OpenTreeOfLife/reference-

4/13/16

4/11/16

Generic URL for a taxon

Is there a generic URL I can use to jump to an OTT node on the latest version of the online tree. Eg

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Generic URL for a taxon

Is there a generic URL I can use to jump to an OTT node on the latest version of the online tree. Eg

4/11/16

Yan Wong, Jonathan A Rees3

4/11/16

strange sources

On Sunday, 3 April 2016 17:26:49 UTC+1, Jonathan Rees wrote: Nope, these are all intended. Ah - OK.

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strange sources

On Sunday, 3 April 2016 17:26:49 UTC+1, Jonathan Rees wrote: Nope, these are all intended. Ah - OK.

4/11/16

4/2/16

"The Path" - Artwork based on the Open Tree of Life

I found out about this project last September when you published the draft version, and was inspired

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"The Path" - Artwork based on the Open Tree of Life

I found out about this project last September when you published the draft version, and was inspired

4/2/16

3/30/16

beta versions of new tree, APIs

We will release the next version of the synthetic tree and the APIs next week. If you want a sneak

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beta versions of new tree, APIs

We will release the next version of the synthetic tree and the APIs next week. If you want a sneak

3/30/16

Ubirajara Oliveira, Karen Cranston2

3/28/16

tree with phylogeny-only tips

Within the next week. Is that soon enough? On Mon, Mar 28, 2016 at 12:12 PM Ubirajara Oliveira <

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tree with phylogeny-only tips

Within the next week. Is that soon enough? On Mon, Mar 28, 2016 at 12:12 PM Ubirajara Oliveira <

3/28/16

Arlin Stoltzfus

3/17/16

phylotastic mobile app - request for alpha testers

Hello all. The first soft release of the phylotastic mobile app is due out next week. The workflow is

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phylotastic mobile app - request for alpha testers

Hello all. The first soft release of the phylotastic mobile app is due out next week. The workflow is

3/17/16

3/15/16

hangout tomorrow

A reminder to core folks about the hangout tomorrow. I assume that we are all plowing forward with

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hangout tomorrow

A reminder to core folks about the hangout tomorrow. I assume that we are all plowing forward with

3/15/16

3/14/16

spec for v3 APIs

The spec for version 3 of the APIs is now finalized. Once implemented, this will allow for both

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spec for v3 APIs

The spec for version 3 of the APIs is now finalized. Once implemented, this will allow for both

3/14/16

François Michonneau, Karen Cranston3

3/10/16

Number of studies

Perfect, thanks! On Thu, Mar 10, 2016 at 11:38 AM, Karen Cranston <karen.c...@gmail.com>

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Number of studies

Perfect, thanks! On Thu, Mar 10, 2016 at 11:38 AM, Karen Cranston <karen.c...@gmail.com>

3/10/16

Ubirajara Oliveira, Karen Cranston3

3/8/16

Dear Karen, In the fact, I need only of the tree with phylogeny-only tips. I look forward the release

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Dear Karen, In the fact, I need only of the tree with phylogeny-only tips. I look forward the release

3/8/16

2/18/16

new conflict service

We just deployed a new conflict service in the OpenTree web application. For any published tree in

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new conflict service

We just deployed a new conflict service in the OpenTree web application. For any published tree in

2/18/16

1/15/16

communication changes

Hello opentree mailing list subscribers, We've made some changes to our communication channels

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communication changes

Hello opentree mailing list subscribers, We've made some changes to our communication channels

1/15/16

Karen Cranston, … Tony Rees5

1/12/16

taxonomy browser

Hi Jonathan, To me it would make sense if the default sort were to be grouped by rank high-low, then

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taxonomy browser

Hi Jonathan, To me it would make sense if the default sort were to be grouped by rank high-low, then

1/12/16

Yan Wong, Jonathan A Rees2

12/28/15

Duplicate scientific names in tree

Agreed, these could all use some attention. I see no automated fix, so each case will require TLC.

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Duplicate scientific names in tree

Agreed, these could all use some attention. I see no automated fix, so each case will require TLC.

12/28/15

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