User: jhc

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jhc2.7k
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Posts by jhc

<prev • 119 results • page 1 of 12 • next >
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Answer: A: Compare topologies of trees with non-identical tip labels
... you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/ ...
written 8 days ago by jhc2.7k
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Job: Postdoctoral positions in Comparative Metagenomics and Phylogenomics at CBGP (Madrid, Spain)
... The CBGP is seeking for outstanding candidates for postdoctoral researcher positions in the CBGP Computational-Systems Biology and Genomics Program (CSBGP). The Center for Plant Biotechnology and Genomics (CBGP), a joint research institute from Universidad Politécnica de Madrid (UPM) and the Instit ...
metagenomics job phylogenomics written 10 weeks ago by jhc2.7k
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Job: Junior Group Leader position in Computational Systems Biology and Genomics at CBGP (Madrid, Spain
... **CBGP is seeking** for a new Group Leader to cover one of the following research areas: Genomic Assisted Breeding Computational Structural Biology Synthetic and Systems Biology We are looking for a highly motivated and productive scientist at Junior level to initiate a recognized research group i ...
systems biology job genomics computational biology written 10 weeks ago by jhc2.7k
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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 3 months ago by jhc2.7k
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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 5 months ago by jhc2.7k
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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 6 months ago by jhc2.7k
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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 6 months ago by jhc2.7k
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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 12 months ago by jhc2.7k
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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 13 months ago by jhc2.7k
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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 14 months ago by jhc2.7k

Latest awards to jhc

Popular Question 10 weeks 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 4 months ago, created an answer with at least 3 up-votes. For A: etetoolkit, Visualization of phylogenetic trees
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 5 months ago, created a post with more than 5 votes. For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: etetoolkit, Visualization of phylogenetic trees
Teacher 14 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 15 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 15 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
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?
Teacher 16 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 16 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 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: Program for searching for a specific partition within a set of phylogenetic tree
Scholar 21 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 Plot Go Data Using R Or Any Tools?
Centurion 21 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 22 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 2.1 years 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 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Teacher 2.5 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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