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So I've encountered two problems with users who use macOS:
- SED error when running PhyloGenes
- The "if" condition in the loop for some reason isn't working, even though that comparison should
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I have already sequenced a batch of yeast data and would like to use Haplocheck to detect contamination in the WGS data. I note that the examples mentioned in _Contamination detection in sequencing st…
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Phylotree.js has a "Collapse Subtree" option. We can use this to highlight a particular clade by collapsing all other clades in the phylogeny.
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Hello,
I am trying to make a phylotree for a small dataset with 70 species but keep getting the error message: "Error in -phylo.maker(sp.list = example, tree = GBOTB.extended, nodes = nodes.info.1,…
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A user recently sent me a tree and was astounded by what he is seeing in PATRIC, so I had to tell him that I always take the newick file and visualize the tree in FigTree due to this problem, but its …
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I would like to use HaploGrep to classify a FASTA sample with respect to the RSRS, but the option does not seem to work. I get the error:
`[classify, --in, simulations/Q1.fa, --out, here, --format,…
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I try to use phylotree.js in an npm environment trying to render newick files. Unfortunately, I can't get it to work and the documentation of the project seems to be somewhat broken. In particular, th…
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When calling Tree.render() like this:
treedata is a newick string
t = Tree(treedata)
base64_img, img_map = t.render("%%return.PNG", tree_style=style)
I get an error:
AttributeError: 'TreeNode…
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Hi
I wonder if this is possible to pre-color some nodes/branches at load time.
I use the NHX format for this, and to store other kind of information, but NHX tags look to be ignored by phylotree.j…
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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…