[Primeusers] syntax and tree input problems

[A.Malhotra]

I am using the new binaries distributed in Feb 2012 and am having 
trouble getting my species treefile read, and also with my syntax for 
some of the options. I would be grateful if anyone can set me right on 
these issues.

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);

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.

Thanks in anticipation!
Anita
-- 
*******************************************************************
Dr Anita Malhotra         	e-mail: a.malhotra at bangor.ac.uk
School of Biological Sciences	Tel(direct line): + 44 1248 383735
College of Natural Sciences	Fax: + 44 1248 371644
Bangor University		
3rd Floor ECW
Deiniol Road, Bangor		
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United Kingdom
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