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Re^5: phylogenetic tree construction using perl

by jgamble (Pilgrim)
on Oct 02, 2012 at 14:23 UTC ( #996865=note: print w/replies, xml ) Need Help??


in reply to Re^4: phylogenetic tree construction using perl
in thread phylogenetic tree construction using perl

I'm only able to look at the paper in my spare time, and I had no spare time for the past few days. Also, quite frankly, I didn't know if your problem had been solved already or not.

Did the bioperl suggestions lead anywhere for you?

I'll resume reading the paper tomorrow. If you have any further reading material that might be helpful, please let me know. I can be reached more directly at jgamble@cpan.org.

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Re^6: phylogenetic tree construction using perl
by zing (Beadle) on Oct 02, 2012 at 17:11 UTC
    No Sir, Its not solved yet. Actually as previously wrote its the implementation of Alfred Aho's algorithm so as to construct a phylogenetic tree.The algorithm is there in section 7.2.3 of the paper. Sir thats the only material/paper Im following right now.

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[LanX]: not my code ...
[choroba]: yeah, sounds like one of the strings is not flagged as UTF-8
[choroba]: which usually means its input wasn't handled correctly
[Corion]: choroba: Yeah, I think that would be the good solution
[LanX]: I suspect the first string which comes from the DB ...
[LanX]: ... but this part is already in production for a year now
[Corion]: LanX: The "good" approach here would be to use the appropriate DBI parameters to make the driver decode strings properly. But that will have a ripple-on effect of messing up all the places where manual decoding happens ;)
[LanX]: which means albeit being broken UTF8 it'll be handled correctly
[LanX]: and the problem only occurs since we changed the emails to base64
[LanX]: my main problem will be to cnvince my colleagues that our productive code is broken oO ... so in the end I will just make a workaround :-/

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