User: neutrinoscientist

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Posts by neutrinoscientist

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3D bipartite Network visualization
... I have a dataset of microbes and phenotype. And I want to create a 3D bipartite network visualization using javascript. Any help in how to implement this and which lib I should use? I found that d3 implements this but in 2D. I tried to search similar questions, but didn't find any. Any help pleas ...
next-gen written 6 months ago by neutrinoscientist0 • updated 12 weeks ago by guangyan.zh00
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Comment: C: Phylogeny tree from a set of taxa
... its, a phylogeny tree (species and their classification: kingdom, phylum, class, order ....) ...
written 9 months ago by neutrinoscientist0
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Comment: C: Phylogeny tree from a set of taxa
... excuse me what you mean by relevant sequences? ...
written 9 months ago by neutrinoscientist0
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Phylogeny tree from a set of taxa
... I have set of taxa and I want to generate dynamically a phylogeney tree file based on a reference database. EX. the users will choose the set of taxa that they're interested in, from ~1000 taxa and the I should create the corresponding phylogeney tree. are there any R packages to create a tree fro ...
taxa species phylogenetic tree newick taxonomy written 9 months ago by neutrinoscientist0 • updated 9 months ago by Jean-Karim Heriche18k
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Phylogeny Tree based on SILVA classification
... Hello, have a list of species (taxa) and i want to generate a phylogeny tree using SILVA. How to do this? any help please. Thanks. ...
taxonomy written 9 months ago by neutrinoscientist0 • updated 9 months ago by Chirag Parsania1.4k
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Comment: C: How to convert tree in phylip format into newick format
... I have a tree in phylip format and i want to convert it to newick format ...
written 10 months ago by neutrinoscientist0
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Comment: C: How to convert tree in phylip format into newick format
... not working Traceback (most recent call last): File "convert_trees.py", line 9, in Phylo.convert(infile,intype, outfile, outtype) File "/home/maria/.local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 90, in convert return write(trees, out_file, out_format, **kwargs) File "/hom ...
written 10 months ago by neutrinoscientist0
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Comment: C: How to convert tree in phylip format into newick format
... python convert_trees.py phyliptree.phy phylip mytree.nwk newick ...
written 10 months ago by neutrinoscientist0 • updated 10 months ago by h.mon24k
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Comment: C: How to convert tree in phylip format into newick format
... am so sorry for adding this as an answer. sorry its just in mistake. its still give error. Traceback (most recent call last): File "convert_trees.py", line 9, in Phylo.convert(infile,intype, outfile, outtype) File "/home/x/.local/lib/python2.7/site-packages/Bio/Phylo/_io.p ...
written 10 months ago by neutrinoscientist0 • updated 10 months ago by h.mon24k
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Comment: A: How to convert tree in phylip format into newick format
... File "/home/x/.local/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 234, in write raise ValueError("Unknown format '%s'" % format) ValueError: Unknown format 'newick' any help? ...
written 10 months ago by neutrinoscientist0 • updated 10 months ago by genomax63k

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