User: jhc
jhc • 2.5k
- 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
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 7 days ago by
jhc • 2.5k
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
jhc • 2.5k
0
votes
3
answers
138
views
3
answers
... for NCBI trees, check [ete-ncbiquery][1]
[1]: http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 8 weeks ago by
jhc • 2.5k
0
votes
2
answers
268
views
2
answers
... related: Method description and benchmark comparison against BLAST, interPro and CAFA2 https://doi.org/10.1093/molbev/msx148 ...
written 11 weeks ago by
jhc • 2.5k
3
votes
2
answers
268
views
2
answers
... eggNOG just released [eggnog-mapper][1], a tool for (meta)-genome functional annotation:
[1]: http://eggnog-mapper.embl.de ...
written 12 weeks ago by
jhc • 2.5k
0
votes
2
answers
247
views
2
answers
... http://eggnogdb.embl.de/#/app/downloads
...
written 3 months ago by
jhc • 2.5k
1
vote
0
answers
170
views
0
answers
... see this: https://www.biostars.org/p/240409/#240438 ...
written 3 months ago by
jhc • 2.5k
3
votes
3
answers
244
views
3
answers
... 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
jhc • 2.5k
5
votes
2
answers
247
views
2
answers
... 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
jhc • 2.5k
2
votes
4
answers
362
views
4
answers
... 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
jhc • 2.5k
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.
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
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
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?
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