Phylogenetic Tree
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9.1 years ago

Hello,

Could anyone suggest the good phylogenetic tree reading program (Where I can manually sketch/write something that I want)?

Thanks!

phylogenetics tree parser • 3.1k views
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9.0 years ago

If you mean "I know the topology and perhaps also branch lengths of a particular tree I'm interested in, and want to turn that into an (e.g. NEWICK format) tree file, whose representation I want to then manipulate in a tree viewer such as Dendroscope or FigTree"

then you could try using Mesquite http://mesquiteproject.org/mesquite/mesquite.html .

It takes some practice to get used to it, but maybe you'll find these notes I've put together on it useful http://www.embl.de/~seqanal/courses/commonCourseContent/usingMesquite.html

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9.1 years ago

use Bio::TreeIO to read the tree, save it to SVG , edit it with inkscape

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9.1 years ago

... or ITOL if you want a web-app and don't like to script, then save to SVG

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9.1 years ago
ALchEmiXt ★ 1.9k

Maybe SplitsTree can do what you want... There you can conveniently rotate and move clades/nodes while preserving branch lengths....and more.. It can start with all sorts of formats from distance matrices to PHILIP, nexus asf...

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5.7 years ago

I recommend Bosque. You can view adn edit newick trees very easy.

http://inf.imo-chile.cl/software/bosque.html

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5.2 years ago

I would recommend PhyML for tree generation, figtree for edition and visualization and inkscape for final ajustments

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