Knuckles in extracted synthetic tree

[opentreeoflife]

Knuckles in extracted synthetic tree

[jar398]

sorry, what's a "knuckle" exactly?

On Tue, Jul 23, 2013 at 11:32 AM, Joseph W. Brown
[email protected]:

Synthetic tree retains "knuckles" or "knees" present in taxonomy. These
are not handled by any analyses wanting to use the trees (although viewers
like Dendroscope and FigTree can display them). For now, just use scripts
to remove these. Eventually has as an export option.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/49
.

[josephwb]

A non-splitting node; say, a family with just one genus. That is, it has
one parent, and one child.

JWB.

On 26 July 2013 17:51, Jonathan A Rees [email protected] wrote:

sorry, what's a "knuckle" exactly?

On Tue, Jul 23, 2013 at 11:32 AM, Joseph W. Brown
[email protected]:

Synthetic tree retains "knuckles" or "knees" present in taxonomy. These
are not handled by any analyses wanting to use the trees (although
viewers
like Dendroscope and FigTree can display them). For now, just use
scripts
to remove these. Eventually has as an export option.

—
Reply to this email directly or view it on GitHub<
https://github.com/OpenTreeOfLife/treemachine/issues/49>
.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/49#issuecomment-21650398
.

[josephwb]

This is going to need to be addressed, as software other than Dendroscope cannot handle knuckles/knees. I know that @blackrim has some code (python?) that does this, but we need to have it in treemachine. I'm happy to recode it in java.

[blackrim]

hm, a problem with this though is that what do you do with the knuckles.
you can remove them but you lose information (taxon names that are often
searched for)
On Wed, Apr 16, 2014 at 10:19:03AM -0700, Joseph W. Brown wrote:

This is going to need to be addressed, as software other than Dendroscope cannot handle knuckles/knees. I know that @blackrim has some code (python?) that does this, but we need to have it in treemachine. I'm happy to recode it in java.

---

Reply to this email directly or view it on GitHub:
#49 (comment)

Dr. Stephen A. Smith
http://blackrim.org
Assistant Professor, Dept. Ecology and Evolutionary Biology
University of Michigan
2071A Kraus Natural Science Building
830 North University
Ann Arbor, MI 48109-1048

[josephwb]

Right. A monotypic order will lose everything except the Genus_species info. But you can't even get a knuckled tree into, say, R.

Concatenating taxonomic levels into the tip name:

Order_Family_Genus_species

would work for the monotypic example, but would be cumbersome for, say, a diverse genus in an order with just one family.

I don't know what the correct solution is here...

[rhr]

I can understand why a tree inference program might not accept trees with
knuckles, but not scripting libraries or tree viewers. Strange design
choice.

On Wed, Apr 16, 2014 at 1:35 PM, Joseph W. Brown
[email protected]:

Right. A monotypic order will lose everything except the Genus_species
info. But you can't even get a knuckled tree into, say, R. Concatenating
taxonomic levels into the tip name:

Order_Family_Genus_species

would work for the monotypic example, but would be cumbersome for, say, a
diverse genus in an order with just one family.

I don't know what the correct solution is here...

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/49?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40635340
.

[chinchliff]

What are the use cases for trees with (taxonomically named) knuckles?

We could always just provide the knuckle option, and default to excising
them (or vice versa).

On Wed, Apr 16, 2014 at 2:43 PM, Rick Ree [email protected] wrote:

I can understand why a tree inference program might not accept trees with
knuckles, but not scripting libraries or tree viewers. Strange design
choice.

On Wed, Apr 16, 2014 at 1:35 PM, Joseph W. Brown
[email protected]:

Right. A monotypic order will lose everything except the Genus_species
info. But you can't even get a knuckled tree into, say, R. Concatenating
taxonomic levels into the tip name:

Order_Family_Genus_species

would work for the monotypic example, but would be cumbersome for, say,
a
diverse genus in an order with just one family.

I don't know what the correct solution is here...

—
Reply to this email directly or view it on GitHub<
https://github.com/OpenTreeOfLife/treemachine/issues/49?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40635340>

.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/49#issuecomment-40636322
.

[blackrim]

I would say the use case would be some reference to the knuckle
like when searching for a taxon, adding taxa from fossils or other
samples one might have (thinking about knuckles around birds). also, if
the knuckles represent nodes that have fossils that we dont' have in
the tree, they might have length I suppose. anyway, it seems like R
might be the only one that doesn't read them, is that right? wondering
if it should be a special export option for R?

On Wed, Apr 16, 2014 at 12:39:13PM -0700, Cody Hinchliff wrote:

What are the use cases for trees with (taxonomically named) knuckles?

We could always just provide the knuckle option, and default to excising
them (or vice versa).

On Wed, Apr 16, 2014 at 2:43 PM, Rick Ree [email protected] wrote:

I can understand why a tree inference program might not accept trees with
knuckles, but not scripting libraries or tree viewers. Strange design
choice.

On Wed, Apr 16, 2014 at 1:35 PM, Joseph W. Brown
[email protected]:

Right. A monotypic order will lose everything except the Genus_species
info. But you can't even get a knuckled tree into, say, R. Concatenating
taxonomic levels into the tip name:

Order_Family_Genus_species

would work for the monotypic example, but would be cumbersome for, say,
a
diverse genus in an order with just one family.

I don't know what the correct solution is here...

—
Reply to this email directly or view it on GitHub<
https://github.com/OpenTreeOfLife/treemachine/issues/49?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email&utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40635340>

.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/49?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40636322
.

---

Reply to this email directly or view it on GitHub:
https://github.com/OpenTreeOfLife/treemachine/issues/49?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40642620

Dr. Stephen A. Smith
http://blackrim.org
Assistant Professor, Dept. Ecology and Evolutionary Biology
University of Michigan
2071A Kraus Natural Science Building
830 North University
Ann Arbor, MI 48109-1048

[josephwb]

I don't know. How else are people going to use these trees?

[josephwb]

We have de-knucklers on our side that could be used. There is a function in the R package phytools, but it is prohibitively slow at the moment. I am talking to Liam about optimizing it. Regardless, we should have something in place by the hackathon.