Missing TNT script ILD.run

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Nick Matzke

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Aug 21, 2015, 8:17:21 AM8/21/15
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Hi all,

I was just attempting to program a quick TNT script to do an ILD test.  I found, to my frustration, that the WayBack machine archive of the tntwiki only saved about half the scripts.

Because I am feeling neurotic today, I decided to dig around the internet from the script. I found some of them, but not ILD.run, the one I need!

Anyway, others might as well benefit from my neurosis, so I have posted what I could find, below.

If you find ILD.run, or any of the other missing scripts, on your hard drive, please email to me, or post the text to the TNT Google Group!

Thanks,
Nick


LONGER VERSION:

The Wayback Machine archive page is here:

However, only some of the .run files are available.  I have put the ones I could find here:


Below are the ones that used to be available at tntwiki, but which were not archived by the WayBack Machine, and I cannot find them anywhere online. If you happen to have a local copy saved, please email them to me at nick....@anu.edu.au if you happen to have them. Several of them are referenced in publications that link to the old TNTwiki, so they ought to be available online somewhere, for purposes of replicability and usability of the scientific literature.

For example:

Scripts referenced in the literature that are no longer available (as far as I can tell):
==================================
blockjak.run is referenced by: 

Mark E. Siddall (2009). "Unringing a bell: metazoan phylogenomics and the partition bootstrap." Cladistics, 26(4), 444-452. 

landcombsch.run is referenced by: 

Hendrickx C, Araújo R, Mateus O. (2014) The nonavian theropod quadrate II: systematic usefulness, major trends and cladistic and phylogenetic morphometrics analyses. PeerJ PrePrints 2:e380v2 https://dx.doi.org/10.7287/peerj.preprints.380v2
==================================

I am also happy to upload any other scripts, if people have new ones.  Wikidot has a perma-backup system so they *should* be safe.  One could also paste any scripts to the TNT Google Group, which would be a pretty permanent form of archiving a script also.


MISSING SCRIPTS -- PLEASE EMAIL TO nick....@anu.edu.au IF YOU HAVE ONE OF THEM
==================================
LandschW.run

Landcombsch.run

blockjak.run

codonweight.run

Ild.run

Deactmiss.run
==================================

Ross Mounce

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Sep 14, 2015, 11:47:16 AM9/14/15
to TNT-Tree Analysis using New Technology
Hi Nick,

I have two versions of TNT scripts for ILD analysis. They are attached. I will upload the rest if I find them.

Side-note:

As first reported in Allard, M.W., Farris, J.S. and Carpenter, J.M. 1999a. Congruence among mammalian
mitochondrial genes. Cladistics 15:75–84

PAUP* & TNT can give significantly different answers for ILD analyses, even with precisely the same parameters & data. When the PAUP* source code is published I shall be very interested to look at how they have implemented the ILD test. I suspect (but cannot prove because neither TNT nor PAUP are open source!) that one of them was implementing the method incorrectly.

PS I thought PAUP was going open source in 2014 but I couldn't find where it is. If you have a link to the source code, please let me know!
https://twitter.com/omearabrian/status/499222031708073985

 
Ild.run
ildtnt.RUN

Nick Matzke

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Sep 15, 2015, 2:41:32 PM9/15/15
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Thanks for these! I will put them in the "Files" section of the phylowiki tnt script page when I get a chance (swamped with job stuff this week).

If people have copies of other scripts that use to be up (or, new ones that they would like to archive), send them along (and/or post to the google group, which should be a pretty permanent archive).

PS: People may be interested in some R code I put up to ease the process of reading TNT trees, statistics, etc., into R:


...this is not really "my job description", so don't necessarily expect help/support/updates on any regular schedule, but it might be handy for some basic things.

Cheers,
Nick





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Nick Matzke

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Sep 25, 2015, 8:10:19 AM9/25/15
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Hi all,

I have uploaded the ILD scripts, and also a script for the Templeton Test, contributed by Alexander Schmidt-Lebuhn:


Thanks to both of you!

Cheers,
Nick


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