Problems calculating the CI and RI index

[ENRIQUE TORRES PARISH]

Hi everybody. I'm having some problems trying to calculate the consistency index (CI) and retention Index (RI). I know that I have to use the stats.run but for some reason I don't have the extension, instead I have the aquickie.run but it does't do the same job. 

May be it's because the 1.6. version was incomplete by the time I dowloaded, I honestly don't know. How can I dowloud the stats.run for the 1.6?. 

By the way if there is an other method to calculate the CI and RI, pls let me know, I'm still figuring out how to work with TNT

[René Dederichs]

Hello enrique, 

have you tried to 'open' the run data? Normally when i use open file > choose the .run data it should work.

Otherwise perhaps a new download would solve the problem.

Cheers

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[Nick Matzke]

Hi!

stats.run and many (not all) of the old scripts available on the defunct TNT wiki are here:

http://phylo.wikidot.com/tntwiki

Cheers,

Nick

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[Pedro Peñaherrera]

Hi,

Following the second question....is there any other method to calculate the CI and RI? I'm interested in calculating both indexes per character but when I run the stats I only get the value of my tree, I saw that in some conversations this script should also indicate the CI and RI of each character. 

Hope anyone can help me.

P

[Camilo]

Hi Pedro,

Here you have two scripts to do it:

Charstats.run by Martin Ramirez

Statsall.run by Peterson Lopes
Cheers,
Camilo

[Edward SIddall]

You can always do this yourself character by character. Minsteps = number of states. Maxsteps is found from optimizing on a fully unresolved hard-polytomy bush from tr. Observed steps is, well, steps observed in (say) best tree

CI = min/obs

RI = (max-obs)/(max-min)

Para ver este debate, visita https://groups.google.com/d/msgid/tnt-tree-analysis-using-new-technology/0d750f42-1094-40f8-a9da-46ce24fe8a94n%40googlegroups.com.