User: jhc

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jhc2.6k
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Posts by jhc

<prev • 116 results • page 1 of 12 • next >
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Comment: C: ETE3 compare stop filename truncation
... not possible at the moment. It would require a very small change in the code increasing the max length from 15 to anything else: https://github.com/etetoolkit/ete/blob/da6a23ae7adbe98be26a232a29fd90af3a66b0b5/ete3/tools/ete_compare.py#L185 ...
written 9 days ago by jhc2.6k
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Answer: A: Ultrametric tree in ete3 (python)
... try something like this: from ete3 import Tree def is_ultrametric(tree): last_distance = None distance = 0 for post, node in tree.iter_prepostorder(): if post: distance -= node.dist else: if not node.is ...
written 10 weeks ago by jhc2.6k
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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 3 months ago by jhc2.6k
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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]. **(closed)** 2. PhD in comparative metagenomics via INPhiNIT program **(closed)** 3. Postdoc in ...
gene function metagenomics job phylogenomics written 3 months ago by jhc2.6k
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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 9 months ago by jhc2.6k
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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 10 months ago by jhc2.6k
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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 11 months ago by jhc2.6k
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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 11 months ago by jhc2.6k
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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 11 months ago by jhc2.6k
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Comment: C: What are those "ENOG" numbers in eggNOG 4.5?
... http://eggnogdb.embl.de/#/app/downloads ...
written 12 months ago by jhc2.6k

Latest awards to jhc

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: etetoolkit, Visualization of phylogenetic trees
Scholar 10 weeks ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: etetoolkit, Visualization of phylogenetic trees
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?
Popular Question 12 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 12 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
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?
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?
Scholar 13 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: Program for searching for a specific partition within a set of phylogenetic tree
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 18 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 18 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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Scholar 18 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 19 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Appreciated 22 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 22 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 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?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs

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