User: jhc

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jhc2.4k
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Posts by jhc

<prev • 103 results • page 1 of 11 • next >
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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 12 days ago by jhc2.4k
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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 8 weeks ago by jhc2.4k
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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 12 weeks ago by jhc2.4k
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Comment: C: Find orthologs using EggNOG and local HMMER search for multiple transcripts
... Most probably, many of your nucleotide seqs are not in the correct frame or are not the complete CDS. My suggestion is: translate the set of nucleotide sequences using a dedicated tool, review that the protein products make sense, and upload the protein set to eggnog mapper. ...
written 3 months ago by jhc2.4k
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Comment: C: Find orthologs using EggNOG and local HMMER search for multiple transcripts
... no, that option was not enabled yesterday. But, even now, upload protein sequences if possible. translation is automatic and if the CDS sequence is not correctly formatted you will miss annotations. ...
written 3 months ago by jhc2.4k
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Comment: C: Find orthologs using EggNOG and local HMMER search for multiple transcripts
... I just added this option. Nucleotide sequences should now be accepted and automatically translated. ...
written 3 months ago by jhc2.4k
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Answer: A: Find orthologs using EggNOG and local HMMER search for multiple transcripts
... There is now a better resource for functional annotation using eggNOG orthology. Check these links: *Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper* - http://eggnog-mapper.embl.de (online tool) - http://biorxiv.org/content/early/2016/09/22/076331 (method de ...
written 3 months ago by jhc2.4k
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Answer: A: Tree file and taxonomy
... If you have access to the taxID of each sequence, you could annotate trees using ete3: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html#automatic-tree-annotation-using-ncbi-taxonomy check also the ete-ncbiquery and ete-annotate command line tools: http://etetoolkit.org/document ...
written 3 months ago by jhc2.4k
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Answer: A: subtree corresponding to ev.etype
... the event instance obtained when calling 'get_my_evol_events()' or 'get_descendant_evol_events' [contains a pointer to the corresponding internal node][1]: an example [based on the tutorial][2]: from ete3 import PhyloTree nw = "((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu ...
written 3 months ago by jhc2.4k
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Comment: C: treefix tree output format conversion
... ete3 can read newick files even if there are new lines and spaces in it. use tree.write() to export back in a clean newick string. ...
written 3 months ago by jhc2.4k

Latest awards to jhc

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
Centurion 12 weeks ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated 4 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Teacher 6 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 6 months ago, created an answer that was upvoted at least 5 times. For A: Parsing A Tree File
Appreciated 7 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
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?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 12 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Label Internal Branches Of A Phylogenetic Tree?
Scholar 12 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 Label Internal Branches Of A Phylogenetic Tree?
Scholar 13 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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?
Scholar 17 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
Appreciated 18 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
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?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Parsing A Tree File
Voter 19 months ago, voted more than 100 times.

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