-
In an effort to write unit testing for the Newick file importer that comes with Tripal, do you have a file that could be shared? We would need the file in newick format, a FASTA file containing all o…
-
I am trying retrieve the taxonomy for Chordata using the web services. I used this command line:
``` bash
curl -X POST http://api.opentreeoflife.org/v2/taxonomy/subtree -H 'Content-type:application/j…
-
This bug happens due to extra parentheses in the Newick string. You can replicate it…
arlin updated
7 years ago
-
Hey all!
I am interested in examining some of the main transfer events in my species tree-gene tree reconciliation, but both .xml and .nhx gives me all the transfer events. I was wondering if it's …
-
I've been trying to use `tree.getNewick()` to implement a custom menu item in phylotree.js v1.4.0 that can be used to rename a node. The [algorithm I use](https://github.com/phyloref/klados/blob/ef276…
-
I think it is important to have a way to check file formats beyond assuming file extensions are correct.
For example if .phy is reserved for newick and .tre for nexus format trees, then if I use an e…
-
Besides issue #234 , there is another problem with Bio::TreeIO.
When parsing a Newick formatted file in which the internal node names are bootstrap support values, and the attempting to write the res…
-
...
2021-03-13 16:16:44 : Written final scores for species 117 to graph file
2021-03-13 16:16:45 : Written final scores for species 110 to graph file
2021-03-13 16:16:45 : Written final scores fo…
-
Hello all,
I have the best bootstrap tree with values overlaid on branches ("nodes"), as output from RAxML.
The tree encodes the bootstrap values within square brackets, just after the branch le…
-
Hi,
I tried to follow the vignette to convert a dataframe to Newick format, but I the branch length in the output are wrong, although the overall shape of the tree is correct.
This is my current d…