[Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Florent Angly
florent.angly at gmail.com
Fri Feb 5 21:56:56 EST 2010
Hi,
I've used Bio::Phylo for drawing SVG trees non-interactively. It's not
part of Bioperl but draws nice trees:
http://search.cpan.org/~rvosa/Bio-Phylo/
<http://search.cpan.org/%7Ervosa/Bio-Phylo/>
Florent
On 02/10/07 05:32, Jason Stajich wrote:
> I'd definitely recommend Bio::Tree::Draw::Cladogram over svggraph
> for prettier trees - you get postscript out but you can render this
> to png or jpg with unix tools. If there is a better stand alone tree
> drawing engine we're happy to try and integrate it into bioperl - the
> modules here are native Perl only and you can use the bioperl-run
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS
> rendering output.
>
> Mesquite, TreeView or other tools are usually much better but not
> always an option if you want to auto-render these images for a
> website, etc.
>
> -jason
>
>
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
>
>
>> Yes,
>> that's the issue about those commands, trees are not pretty at all
>> that's why for a one tree only kind of thing I rather use ITOL
>> other thing to try is the tree drawer of the Mesquite package
>> glad I could help
>>
>> Lucia
>>
>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>
>>
>>> Dear Lucia,
>>>
>>> Thanks for the mail. Now I got it. I didnt used this TreeIO /
>>> Tree::Draw
>>> methods. Some how missed this excellent HOWTO :
>>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as
>>> well. I
>>> tried that and it worked very nicely. I have to work around to
>>> beautify
>>> the tree and I am just going to do that.
>>>
>>> Thanks& Cheers,
>>> Shameer
>>>
>>>
>>>> OK
>>>>
>>>> you can use the implementations in Bio::TreeIO
>>>>
>>>> you can basically read the tree in newick format and out as an
>>>> svg graph
>>>> something like this:
>>>>
>>>> my $in = new Bio::TreeIO(-file => 'input',
>>>> -format => 'newick');
>>>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>>>> -format => 'svggraph');
>>>> while( my $tree = $in->next_tree ) {
>>>> $out->write_tree($tree);
>>>> }
>>>>
>>>> you can also use Bio::Tree::Draw
>>>>
>>>> hope that helps
>>>>
>>>> Lucia
>>>>
>>>>
>>>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> Thanks for your mail. I have to create these trees as a part of a
>>>>> webserver. i need to generate them dynamically using users input
>>>>> sequence.
>>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>>
>>>>>
>>>>>> I think you'll have better luck using some of already available
>>>>>>
>>>>> programs
>>>>>
>>>>>> to do
>>>>>> that, you'll get better looking trees. If you just have one
>>>>>> tree to
>>>>>>
>>>>> draw I
>>>>>
>>>>>> recommend you use:
>>>>>> http://itol.embl.de/
>>>>>>
>>>>>> Lucia
>>>>>>
>>>>>>
>>>>>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>>>>>
>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>>>>>
>>>>> Bioperl
>>>>>
>>>>>>> ?
>>>>>>> My input file are in phylip treefile format. Any Modules /
>>>>>>> codes in
>>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>>
>>>>>>> Input file :
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,
>> (((((((_E_499_500:2.75000,_E_250_251:2.75000):
>> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):
>> 1.51514,_H_255_263:6.20895):0.83877,
>> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772):
>> 0.92645,_H_520_534:7.97418):0.15279,
>> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):
>> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,
>> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):
>> 0.50000,_L_445_447:7.75000):0.50300):1.08808,
>> (((((_E_381_382:2.65000,_E_377_378:2.65000):
>> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):
>> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):
>> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):
>> 1.52226,_H_463_464:5.42226):0.94093,
>> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319):
>> 1.64489,_L_336_343:8.00808):0.88402,
>> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,
>> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,
>> (((((_E_470_474:3.85000,_E_344_348:
>>
>>>>> 3.
>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>> 85000):0.89054,_L_475_478:4.74054):1.20107,
>> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161):
>> 0.71112,_L_513_519:6.65273):0.67204,
>> ((_L_296_304:5.00000,_H_292_295:5.00000):
>> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):
>> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):
>> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,
>> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):
>> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):
>> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):
>> 1.08193,_H_229_243:7.93459):0.18730,
>> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,
>> ((((_H_159_171:7.00000,_L_156_158:7.00000):
>> 0.07448,_L_120_122:7.07448):1.59389,
>> ((((_L__90__91:2.65000,_E__88__89:2.65000):
>> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):
>> 1.74719,_L_147_155:6.52780):2.14057):2.44189,
>> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,
>> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544):
>> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>
>>>>> 5
>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,
>> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,
>> ((((_L_108_109:4.30000,_E_104_107:4.30000):
>> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,
>> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,
>> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,
>> (((((_H___3___6:3.30000,_L___1___2:3.30000):
>> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):
>> 0.88488,_E__40__48:5.79344):0.60814,
>> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):
>> 1.25080):0.17461):6.94325);
>>
>>>>>>>
>>>>> --
>>>>> Shameer Khadar
>>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>>> National Centre for Biological Sciences (TIFR)
>>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>>> T - 91-080-23666001 EXT - 6251
>>>>> W - http://www.ncbs.res.in
>>>>>
>>>>>
>>>>
>>>> Lucia Peixoto
>>>> Department of Biology,SAS
>>>> University of Pennsylvania
>>>>
>>>>
>>>
>>> --
>>> Shameer Khadar
>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>> National Centre for Biological Sciences (TIFR)
>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>> T - 91-080-23666001 EXT - 6251
>>> W - http://www.ncbs.res.in
>>>
>>>
>>
>> Lucia Peixoto
>> Department of Biology,SAS
>> University of Pennsylvania
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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