[Bioperl-l] How to draw Phylogeny Tree using Bioperl ?

Mon Oct 1 18:48:51 UTC 2007

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