User: jhc

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jhc2.5k
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Posts by jhc

<prev • 112 results • page 1 of 12 • next >
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Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 4 months ago by jhc2.5k
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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 5 months ago by jhc2.5k
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Comment: C: Bacterial phylogeny download for a list of species
... for NCBI trees, check [ete-ncbiquery][1] [1]: http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 5 months ago by jhc2.5k
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Comment: C: Metagenomics functional annotation hmmsearch vs Blast ???
... related: Method description and benchmark comparison against BLAST, interPro and CAFA2 https://doi.org/10.1093/molbev/msx148 ...
written 6 months ago by jhc2.5k
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Answer: A: Metagenomics functional annotation hmmsearch vs Blast ???
... eggNOG just released [eggnog-mapper][1], a tool for (meta)-genome functional annotation: [1]: http://eggnog-mapper.embl.de ...
written 6 months ago by jhc2.5k
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Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... http://eggnogdb.embl.de/#/app/downloads ...
written 7 months ago by jhc2.5k
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Comment: C: Are COG IDs consistent across different versions of the eggNOG database?
... see this: https://www.biostars.org/p/240409/#240438 ...
written 7 months ago by jhc2.5k
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Answer: A: Software for counting mutations over a tree
... 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 8 months ago by jhc2.5k
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Answer: A: What are those "ENOG" numbers in eggNOG 4.5?
... 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 8 months ago by jhc2.5k
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Answer: A: Metrics to evaluate tree congruence
... 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 10 months ago by jhc2.5k

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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Popular Question 6 months ago, created a question with more than 1,000 views. For ETE build: from sequences to phylogenetic trees with just a single command line.
Appreciated 7 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar 8 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Program for searching for a specific partition within a set of phylogenetic tree
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar 12 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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Scholar 13 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 22 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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