User: jhc
jhc • 2.5k
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Posts by jhc
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... just the NOG, COGs, arCOGs and KOGs are stable ...
written 10 weeks ago by
jhc • 2.5k
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Answer:
A: EggNOG 4.5 database
... the databases bact_50 and bactNOG are not exactly the same. The first (bact_50) includes all bactNOG groups plus all OGs in children taxonomic levels for bactNOGs including more than 50 sequences (this is to increase HMM resolution in groups that are too large). Something similar occurs with euk vs ...
written 3 months ago by
jhc • 2.5k
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... for NCBI trees, check [ete-ncbiquery][1]
[1]: http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 4 months ago by
jhc • 2.5k
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... related: Method description and benchmark comparison against BLAST, interPro and CAFA2 https://doi.org/10.1093/molbev/msx148 ...
written 4 months ago by
jhc • 2.5k
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... eggNOG just released [eggnog-mapper][1], a tool for (meta)-genome functional annotation:
[1]: http://eggnog-mapper.embl.de ...
written 4 months ago by
jhc • 2.5k
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... http://eggnogdb.embl.de/#/app/downloads
...
written 5 months ago by
jhc • 2.5k
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... see this: https://www.biostars.org/p/240409/#240438 ...
written 6 months ago by
jhc • 2.5k
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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 6 months 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 6 months ago by
jhc • 2.5k
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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 8 months ago by
jhc • 2.5k
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