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Posted on 2005-08-01 15:29:25-07 by rvosa
Ask your questions here.
Dear (potential) Bio::Phylo user,

I am the author of this module. Glad you're interested! At this stage, the module is still quite in flux, so from release to release things might change (and even break your scripts - so be warned!). If anything seems unclear feel free to post your questions here. I will be a notified by email, and I'll get back to you as soon as I can.

Best wishes,
Rutger
Direct Responses: 2788 | Write a response
Posted on 2006-08-16 21:46:21-07 by lupeix23 in response to 820
Re: Ask your questions here.
Hi I've been using your tools a lot, so Bad you missed the meeting at UPENN

But I am not sure if the symetric distance it's geeting it right

Here are 2 almost identical trees, and the sym_dist reported is 23, is that Ok? Visually they are identical

Thanks

The trees:

(((cne531:0.339269,(((((((dme9697:0.023780,aga8870:0.037111)90:0.047976,(cel1016 7:0.000000,cbr5952:0.005627)100:0.157710)100:0.147733,((((mmu2705:0.001373,hsa80 58:0.033284)99:0.038768,rno26599:0.000000)86:0.012921,gga701:0.017695)82:0.01364 3,(dre17976:0.000000,(tni4042:0.000000,fru10354:0.023602)100:0.047009)79:0.01590 1)100:0.086645)98:0.121069,(((((((sce431:0.022073,cgl2990:0.012020)78:0.021273,k la4067:0.042105)70:0.009125,ago4532:0.095439)99:0.071578,dha6577:0.104685)85:0.0 44547,yli6618:0.165663)91:0.096462,ncr8760:0.271286)80:0.139334,tgo4242:0.259948 )27:0.040168)45:0.103778,(((pvi788:0.010532,pkn1748:0.023215)93:0.044149,pyo1354 :0.057499)85:0.056958,pfa555:0.006937)100:0.303054)31:0.046502,ddi13003:0.257905 )28:0.044253,tps8616:0.294314)31:0.036646)100:0.153925,ath9394:0.044374)100:0.09 6928,osa53631:0.006705,osa39710:0.017401);

(((cne531:0.339269,(((((((dme9697:0.023780,aga8870:0.037111)89:0.047976,(cel1016 7:0.000000,cbr5952:0.005627)100:0.157710)100:0.147733,((((mmu2705:0.001373,hsa80 58:0.033284)98:0.038768,rno26599:0.000000)73:0.012921,gga701:0.017695)81:0.01364 3,(dre17976:0.000000,(tni4042:0.000000,fru10354:0.023602)100:0.047009)67:0.01590 1)100:0.086645)100:0.121069,(((((((sce431:0.022073,cgl2990:0.012020)81:0.021273, kla4067:0.042105)66:0.009125,ago4532:0.095439)98:0.071578,dha6577:0.104685)90:0. 044547,yli6618:0.165663)92:0.096462,ncr8760:0.271286)75:0.139334,tgo4242:0.25994 8)24:0.040168)35:0.103778,(((pvi788:0.010532,pkn1748:0.023215)93:0.044149,pyo135 4:0.057499)81:0.056958,pfa555:0.006937)100:0.303054)23:0.046502,ddi13003:0.25790 5)18:0.044253,tps8616:0.294314)28:0.036646)100:0.153925,ath9394:0.044374)100:0.0 96928,osa53631:0.006705,osa39710:0.017401);

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Posted on 2006-08-28 18:07:20-07 by rvosa in response to 2788
Re: Ask your questions here.
I checked your trees. You're right, the symmdiff should be 0. You found a bug. Thank you for bringing this to my attention. I filed it in the bug tracker and will try to have it fixed in version 0.13.
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