[Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Jason Stajich
jason at bioperl.org
Mon Oct 1 19:32:38 UTC 2007
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
More information about the Bioperl-l
mailing list