Is this normal behavior for "pxcltr"

[Cactusolo]

Hi,

I was told that "pxcltr" is meant to remove 'knuckles' (i.e. 2-degree nodes), node annotations, etc, to keep a plain format.

However, I used cmd like:
pxcltr -l -t Coweeta_ottid_nw_rename.tre
and
pxcltr -t Coweeta_ottid_nw_rename.tre

But the results are the same, still keeping some internal labels, eg:

...

|| ++ mrcaott784ott8526
|| || +---------------------------+ Asplenium montanum
|| ||
|| || +----------------------------+ Polypodium virginianum
|| || |
|| |+-++mrcaott8526ott9790---------+ Polystichum acrostichoides
|| | ||
|| ++ mrcaott784ott5078tt21809------+ Dryopteris intermedia
|| || | ++ mrcaott49169ott87323
|| || +-++mrcaott21809ott49169----+ Dryopteris goldiana
|| || |
|| +-+|mrcaott784ott11449-------------+ Dryopteris marginalis
|| | ||
|| | |+-------------------------------+ Adiantum pedatum
|| | |
|| | |+-------------------------------+ Pteridium aquilinum
|| ++ ott56622106
|| || +-------------------------------+ Dennstaedtia punctilobula
|| ||
|| || +--------------------------------+ Osmunda cinnamomea
|| |+-+ ott41629
|+-+ mrcaott784ott3223-----------------+ Osmunda claytoniana
| |
| | +--------------------------------+ Botrychium alabamense
| |+-+ mrcaott33066ott113196
| ++ mrcaott33066ott756444------------+ Botrychium dissectum
| |
| +----------------------------------+ Botrychium virginianum
|
| +-----------------------------------+ Selaginella apoda
|+-+ mrcaott3661ott18736
|| +-----------------------------------+ Isoetes engelmannii
||
++ ott6133720--------------------------+ Lycopodium clavatum
| |
+---ott719013-------------------------+ Lycopodium lucidulum
|
+-----------------------------------+ Lycopodium flabelliforme

Please let me know if you need tree file.

Thanks!

[josephwb]

Sorry but that is unreadable! Do you have the newicks for both input and output?

[Cactusolo]

Yes, here is the input file: 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…

On May 14, 2018, at 14:26, Joseph W. Brown ***@***.***> wrote: Sorry but that is unreadable! Do you have the newicks for both input and output? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHczADI-fk-8VcFctL5Wh-gVNp9g8460ks5tycxmgaJpZM4T-Rwu>.

[josephwb]

As far as I can see all knuckles are removed.

$ pxlstr -t phy.tre 
tree #: 0
rooted: false
binary: false
nterminal: 589
ninternal: 1943
branch lengths: false
rttipvar: NA
treelength: NA
ultrametric: NA
rootheight: NA

$pxlstr -t clean.tre 
tree #: 0
rooted: true
binary: false
nterminal: 589
ninternal: 435
branch lengths: false
rttipvar: NA
treelength: NA
ultrametric: NA
rootheight: NA

As for the node names: phyx treats names and annotations differently. I may not have implemented this fully. Should be a quick fix.

[Cactusolo]

Ok, thanks Joseph! Looking forward to new update then :) Miao

…

On May 14, 2018, at 16:12, Joseph W. Brown ***@***.***> wrote: As far as I can see all knuckles are removed. $ pxlstr -t phy.tre tree #: 0 rooted: false binary: false nterminal: 589 ninternal: 1943 branch lengths: false rttipvar: NA treelength: NA ultrametric: NA rootheight: NA $pxlstr -t clean.tre tree #: 0 rooted: true binary: false nterminal: 589 ninternal: 435 branch lengths: false rttipvar: NA treelength: NA ultrametric: NA rootheight: NA As for the node names: phyx treats names and annotations differently. I may not have implemented this fully. Should be a quick fix. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHczAKDEArE9Vcfe_-oaEVBcaae7meWCks5tyeUdgaJpZM4T-Rwu>.

[josephwb]

Yup this was a loose end #73 (comment). Will fix it this evening. Sorry about the trouble.

[josephwb]

Actually I will get to this tomorrow.

[Cactusolo]

Take your time buddy! No rush ;) Miao

…

On May 14, 2018, at 16:50, Joseph W. Brown ***@***.***> wrote: Actually I will get to this tomorrow. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHczAM3ke833a6J-RYrnPEqT6HDgNMj5ks5tye4YgaJpZM4T-Rwu>.

[josephwb]

Oof. Should be working with this 940b927.

[josephwb]

@Cactusolo please close if this works for you.

[Cactusolo]

Hi, SoI need to update phyx package on my side from github, and then run again, right? Thanks! Miao 2018-05-15 12:15 GMT-04:00 Joseph W. Brown <notifications@github.com>:

…

@Cactusolo <https://github.com/Cactusolo> please close if this works for you. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHczAIMGE8U440K-CoyEyHVsC5nfnNggks5tyv86gaJpZM4T-Rwu> .

-- Dr. Miao Sun Tel: 352 (284) 0928 Email: cactus@ufl.edu Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd, PO. Box 117800, Gainesville, FL 32611-7800, USA.

[Cactusolo]

Hi, I just realized that I have to request for update phyx on our HPC. I'll report to you soon, Miao 2018-05-15 13:14 GMT-04:00 Miao Sun <notifications@github.com>:

…

Hi, SoI need to update phyx package on my side from github, and then run again, right? Thanks! Miao 2018-05-15 12:15 GMT-04:00 Joseph W. Brown ***@***.***>: > @Cactusolo <https://github.com/Cactusolo> please close if this works for > you. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#82 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AHczAIMGE8U440K- CoyEyHVsC5nfnNggks5tyv86gaJpZM4T-Rwu> > . > -- Dr. Miao Sun Tel: 352 (284) 0928 Email: ***@***.*** Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd <https://maps.google.com/?q=1659+Museum+Rd&entry=gmail&source=g>, PO. Box 117800, Gainesville, FL 32611-7800, USA. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#82 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHczAGoodtp4lluRffNcWIeKMrBvCBtbks5tywzngaJpZM4T-Rwu> .

-- Dr. Miao Sun Tel: 352 (284) 0928 Email: cactus@ufl.edu Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd, PO. Box 117800, Gainesville, FL 32611-7800, USA.

[josephwb]

Got it. Although most phyx programs are so lightweight and only run on a single core that I don't see any advantage in putting it on a cluster. But cool that you are!

[Cactusolo]

Thanks man! It works perfectly! 💯 👍

PS, I did most of my work remotely. Though I have home-brewed phyx on my mac, which conveniently not with me today :)

[Cactusolo]

@josephwb I close this issue now, thanks for all the help!