Question: Phylogenetic Tree
1
gravatar for spandankeshav
7.8 years ago by
Finland
spandankeshav80 wrote:

Hello,

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

Thanks!

phylogenetics tree parser • 2.7k views
ADD COMMENTlink modified 3.9 years ago by curiousbiologist40 • written 7.8 years ago by spandankeshav80
3
gravatar for aidan-budd
7.8 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

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

ADD COMMENTlink written 7.8 years ago by aidan-budd1.9k
2
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum131k
1
gravatar for Michael Dondrup
7.8 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

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

ADD COMMENTlink written 7.8 years ago by Michael Dondrup47k
1
gravatar for nonish5
7.8 years ago by
nonish540
European Union
nonish540 wrote:

You can use MATLAB: http://www.mathworks.com/help/bioinfo/ref/phytreeread.html http://www.mathworks.com/help/bioinfo/ref/phytree.html

ADD COMMENTlink written 7.8 years ago by nonish540
1
gravatar for ALchEmiXt
7.8 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

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...

ADD COMMENTlink modified 7.8 years ago • written 7.8 years ago by ALchEmiXt1.9k
1
gravatar for edwin.rodriguez
4.4 years ago by
edwin.rodriguez10 wrote:

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

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

ADD COMMENTlink written 4.4 years ago by edwin.rodriguez10
0
gravatar for Ron
4.0 years ago by
Ron1.0k
United States
Ron1.0k wrote:

ggtree

https://guangchuangyu.github.io/ggtree/documentation/

ADD COMMENTlink written 4.0 years ago by Ron1.0k
0
gravatar for curiousbiologist
3.9 years ago by
France
curiousbiologist40 wrote:

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

ADD COMMENTlink written 3.9 years ago by curiousbiologist40
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