User: jhc
jhc • 2.5k
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Posts by jhc
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... for NCBI trees, check [ete-ncbiquery][1]
[1]: http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 6 days ago by
jhc • 2.5k
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2
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... related: Method description and benchmark comparison against BLAST, interPro and CAFA2 https://doi.org/10.1093/molbev/msx148 ...
written 23 days ago by
jhc • 2.5k
3
votes
2
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207
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... eggNOG just released [eggnog-mapper][1], a tool for (meta)-genome functional annotation:
[1]: http://eggnog-mapper.embl.de ...
written 28 days ago by
jhc • 2.5k
0
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... http://eggnogdb.embl.de/#/app/downloads
...
written 5 weeks ago by
jhc • 2.5k
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... see this: https://www.biostars.org/p/240409/#240438 ...
written 9 weeks ago by
jhc • 2.5k
3
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3
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... This script might be useful: https://gist.github.com/jhcepas/868b1057d9c0b72a57b809a67ad6e4cc
It displays what mutations occurred in each branch. Should be easy to modify to just count.
![enter image description here][1]
[1]: https://cloud.githubusercontent.com/assets/163658/16267090/534671a6-3 ...
written 11 weeks ago by
jhc • 2.5k
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... Original COG, KOG and arCOG IDs are still maintained in eggNOG 4.5 ([example][1]).
The nomenclature of NOGs (non supervised orthologous groups) changed from NOGxxxxxx to ENOG41xxxxx. The "E" identifies the group as eggNOG-produced. 41 identifies the internal eggnog release version. The next 5 chara ...
written 12 weeks ago by
jhc • 2.5k
2
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4
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319
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... perhaps normalized Robinson-Foulds distances help here.
Take a look at the [ete-compare][1] too. It would allow you to compute all those distances very easily from the command line.
[1]: http://etetoolkit.org/documentation/ete-compare/ ...
written 4 months ago by
jhc • 2.5k
0
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1
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316
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... You can take a look at the prune function of [ETE3.][1] It takes care of deleting single child nodes and preserving original branch lengths if necessary:
http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#pruning-trees
http://etetoolkit.org/docs/latest/reference/reference_tree.html#ete3 ...
written 6 months ago by
jhc • 2.5k
4
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1
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... take a look at the new ETE3 features ( http://mbe.oxfordjournals.org/content/33/6/1635 ).
You can either generate phylogenies using predefined workflows or edit existing trees to add as many labels as you need. Then export as extended newick, or tree images. The [Python AP][1]I should integrate well ...
written 7 months ago by
jhc • 2.5k
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