User: jhc

gravatar for jhc
jhc2.5k
Reputation:
2,520
Status:
Trusted
Location:
Germany
Last seen:
3 hours ago
Joined:
5 years, 1 month ago
Email:
j******@gmail.com

Posts by jhc

<prev • 110 results • page 1 of 11 • next >
0
votes
3
answers
84
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 6 days ago by jhc2.5k
0
votes
2
answers
207
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 23 days ago by jhc2.5k
3
votes
2
answers
207
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 28 days ago by jhc2.5k
0
votes
2
answers
177
views
2
answers
Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... http://eggnogdb.embl.de/#/app/downloads ...
written 5 weeks ago by jhc2.5k
1
vote
0
answers
115
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 9 weeks ago by jhc2.5k
3
votes
3
answers
204
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 11 weeks ago by jhc2.5k
5
votes
2
answers
177
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 12 weeks ago by jhc2.5k
2
votes
4
answers
319
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 4 months ago by jhc2.5k
0
votes
1
answer
316
views
1
answers
Answer: A: Removing duplicate leaves/tips from newick tree
... 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 jhc2.5k
4
votes
1
answer
258
views
1
answers
Answer: A: Phylogenetic tree with tagging
... 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 jhc2.5k

Latest awards to jhc

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
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?
Teacher 12 weeks 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 weeks ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 12 weeks 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 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?
Scholar 7 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Centurion 7 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 8 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 11 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 11 months ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Appreciated 11 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 11 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 13 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 16 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 17 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour