User: jhc

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jhc2.5k
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Posts by jhc

<prev • 114 results • page 1 of 12 • next >
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Answer: A: Annotation of taxonomy information in phylogeny tree
... If you have the NCBI taxid code for each species, yes, it is possible to do it with ETE. Check this part of the documentation: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 11 days ago by jhc2.5k
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Job: 3 positions in Computational Genomics at CBGP in Madrid, Spain. (Postdoc, Predoc and Technician)
... 3 positions are available in the Computational Evolutionary Genomics group at CBGP (Madrid, Spain): 1. Research technician to work on bioinformatics tools such as [ETE][1] toolkit or [eggNOG][2]. 2. PhD in comparative metagenomics 3. Postdoc in phylogenomics/metagenomics More info and up ...
gene function metagenomics orthology job phylogenomics written 11 days ago by jhc2.5k
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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 6 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 7 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 8 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 8 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 8 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 9 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 10 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 10 months ago by jhc2.5k

Latest awards to jhc

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?
Popular Question 9 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 9 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 9 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 10 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 10 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 10 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 10 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 15 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 15 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Centurion 15 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 16 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 19 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 19 months ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Appreciated 19 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 19 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 21 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?

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