User: jhc

gravatar for jhc
jhc2.5k
Reputation:
2,520
Status:
Trusted
Location:
Germany
Last seen:
4 days, 16 hours ago
Joined:
5 years, 3 months ago
Email:
j******@gmail.com

Posts by jhc

<prev • 112 results • page 1 of 12 • next >
0
votes
2
answers
247
views
2
answers
Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 7 days ago by jhc2.5k
0
votes
1
answer
115
views
1
answers
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 weeks ago by jhc2.5k
0
votes
3
answers
138
views
3
answers
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 8 weeks ago by jhc2.5k
0
votes
2
answers
268
views
2
answers
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 11 weeks ago by jhc2.5k
3
votes
2
answers
268
views
2
answers
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 12 weeks ago by jhc2.5k
0
votes
2
answers
247
views
2
answers
Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... http://eggnogdb.embl.de/#/app/downloads ...
written 3 months ago by jhc2.5k
1
vote
0
answers
170
views
0
answers
Comment: C: Are COG IDs consistent across different versions of the eggNOG database?
... see this: https://www.biostars.org/p/240409/#240438 ...
written 3 months ago by jhc2.5k
3
votes
3
answers
244
views
3
answers
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 4 months ago by jhc2.5k
5
votes
2
answers
247
views
2
answers
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 4 months ago by jhc2.5k
2
votes
4
answers
362
views
4
answers
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 6 months ago by jhc2.5k

Latest awards to jhc

Teacher 11 weeks 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 3 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 3 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 3 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 4 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 4 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 4 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 4 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 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
Centurion 9 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 10 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Appreciated 13 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 13 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 15 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 18 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 18 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 19 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour