I have a phylogenetic tree containing approx. 2000 sequences. From those I have a selection of approx. 200 sequences.
To visualize their distribution, I would like to "select" those 200 sequences and collapse the rest. What would be the easiest way to do that?
You can use R. It is no trivial task, so best ask somebody from your department who is familiar with R. Sorry, I know no easier way.
use ggtree and phytools > read your tree > check for each node if your desired tip is not a descendant with getDescendants (compare the returned tip numbers with your tree$tip.labels) > if it is not collapse it with ggtree(tree) %>% collapse(node=x) > iterate through all nodes beginning with "oldest" nodes > done
Alternatively you could (much easier) create a group list for your desired tips. Use groupOTU and subsetting to: show only tip labels where you want -or- make all your desired tips in a different colour (like red and bold font size)
https://www.bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html
You can use R. It is no trivial task, so best ask somebody from your department who is familiar with R. Sorry, I know no easier way.
use ggtree and phytools > read your tree > check for each node if your desired tip is not a descendant with getDescendants (compare the returned tip numbers with your tree$tip.labels) > if it is not collapse it with ggtree(tree) %>% collapse(node=x) > iterate through all nodes beginning with "oldest" nodes > done
Alternatively you could (much easier) create a group list for your desired tips. Use groupOTU and subsetting to: show only tip labels where you want -or- make all your desired tips in a different colour (like red and bold font size)
https://www.bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html
Hi,
I'm sure there are many ways you can do this, but probably you have to write a small script. In python there is a phylogenetic tree manipulation library called DendroPy. I've linked an example code which shows how to prune selected taxa from a tree.
So if you want to use python/DendroPy:
(after installing DendroPy)
1. Read your tree.
2. use function prune_taxa_with_labels
3. write out resultant tree.
https://github.com/jeetsukumaran/DendroPy/blob/master/doc/source/examples/prune_taxa_with_labels.py
Hi,
Using TNT software (available at the link below), you can read your matrix and the tree (as nexus files), and using the command: pruntaxa 0/N you can prune the taxa number N from the tree 0. The taxa can be entered as a range using a period, e.g. pruntaxa 0/5.25 will prune taxa 5 to 25 from tree number 0.
Hope this helps.
http://www.lillo.org.ar/phylogeny/tnt/
I'd recommend Figtree as well, if you don't want to mess around too much with the command line.
The Three Graph software is free and very easy to collapse; open your tree, add support values (under File) and under Edit you can choose collapse nodes by support...
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