[Primeusers] syntax and tree input problems

[Joel Sjöstrand]

Hi, and thanks for using PrIME.

> 1. Treefile: problem is reported as "host tree top time must be greater 
> than 0". My species tree was produced using BEAST and saved as a newick 
> file and as far as I can see follows the format exactly. I have also 
> tried writing it in PRIME format but get exactly the same message.
> 
> (viperine:47.6591,(calloselasma:31.6226,(((((ovo_tonk:9.75845,ovo_maka:9.75845):3.45277,(ovo_mont:11.7369,ovo_conv:11.7369):1.47433):7.40536,(prot_mang:16.3629,proto_flav:16.3629):4.25368):3.03057,(okinavensis:22.232,(gloy_brev:20.6856,(SIST_MIL:10.1258,(SIST_CAT_CAT:0.747923,(SIST_CAT_TER:0.654685,SIST_CAT_EDW:0.654685):0.0932386):9.37785):10.5598):1.54641):1.41518):1.96147,(Trim_BORN:20.0445,(((((Crypt_ery:3.45778,(crypt_albo_1:2.68765,(crypt_albo_2:1.07986,crypt_albo_3:1.07986):1.60779):0.770129):8.37888,(crypt_ven:5.72557,crypt_cardamom:5.72557):6.11108):0.742201,(virido_gump:3.95271,virido_stej:3.95271):8.62615):1.81577,(par_hag:9.94782,par_malc:9.94782):4.44681):1.75256,(POP_POP:4.05176,(pop_sab_EM:1.11346,POP_SAB_S:1.11346):2.9383):12.0954):3.89731):5.56412):6.01402):16.0365);
> 

Our reconciliation applications require an edge predating the root. This is typically set to some reasonable value (e.g. perhaps 10%-100% of the root-to-leaf time). You should therefore add a branch length to the root, e.g.:

(A:1.0,(B:0.4,C:0.4):0.6);  =>  (A:1.0,(B:0.4,C:0.4):0.6):0.25;

> 2. Syntax. By deleting various options and trying again I have narrowed 
> it down to a problem with the -Su option. I am writing it like this:
> -Su DNA Pi=0.254 0.283 0.234 0.229 R=0.1087 0.2980 0.0784 0.1029 0.3372 
> 0.0747
> 
> But this produces "Unknown Beep option" (or similar)
> 
> If I replace this string with -Sm JC69 it seems fine.


This seems like a bug in the newer C++ version, our sincere apologies. However, we have a quicker and improved version of PrIME-GSR (a.k.a. PrIME-DLRS) implemented in Java available at http://code.google.com/p/jprime/
The functionality is the same, although the user options are slightly different (e.g. -sm USERDEFINED='DNA;[0.254,0.283,0.234,0.229];[0.1087,0.2980,0.0784,0.1029,0.3372,0.0747]' for your example above). There is also an improved description available there. Perhaps you can try it out?

Best regards,

     Joel Sjöstrand

Ph.D. student, Stockholm University
SciLifeLab
KISP (Karolinska Institute Science Park)
Tomtebodavägen 23 A, Solna
Sweden



-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://mail.sbc.su.se/pipermail/primeusers/attachments/20120731/c7204c0c/attachment.html