Re: module Bio::TreeIO

Liam Elbourne <[email protected]> Wed, 11 May 2016 12:36:21 +1000
Newsgroups	gmane.comp.lang.perl.bio.general
Message-ID	<[email protected]>
I’m sure it is, just a another case of reinventing the wheel taking less time than reading the manual….


Liam.



> On 11 May 2016, at 12:18 PM, Fields, Christopher J <[email protected]> wrote:
> 
> I think this functionality (mapping from long name to short PHYLIP-compatible and back) is in bioperl.  Would have to dig it up but I recall support being added many moons ago.
> 
> chris
> 
>> On May 10, 2016, at 8:30 PM, Liam Elbourne <[email protected] <mailto:[email protected]>> wrote:
>> 
>> I think it is 10 characters (sequence starts at character 11), not that two characters is worth quibbling about, I just map the original names to hex numbers (which I think is likely to cover the number of sequences one can realistically align…), and then swap out the hex codes when I’ve finished with the alignment/tree etc, for what that is worth…
>> 
>> Liam.
>> 
>> 
>> 
>> 
>> 
>>> On 11 May 2016, at 9:00 AM, Torsten Seemann <[email protected] <mailto:[email protected]>> wrote:
>>> 
>>> I only have a distance matrix derived from Mash and so I need a program to
>>> make a tree from distances.  I do not think I can use RAxML or Mr. Bayes,
>>> right?
>>> 
>>> The PHYLIP format can be used for distance matrices, and PHYLIP has various tools to build trees from them:
>>> 
>>> http://evolution.genetics.washington.edu/phylip/progs.data.dist.html <http://evolution.genetics.washington.edu/phylip/progs.data.dist.html>
>>> 
>>> The MASH dist output file is VERY close to being a valid .PHY file (If taxnames <= 8 chars) but Brian Ondov seems unwilling to implement it within MASH - see my issue here: https://github.com/marbl/Mash/issues/9 <https://github.com/marbl/Mash/issues/9>
>>> 
>>> Torst
>>> 
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