User: jhc

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jhc2.5k
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Posts by jhc

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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 19 hours 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 19 days ago by jhc2.5k
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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 22 days ago by jhc2.5k
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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 10 weeks ago by jhc2.5k
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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 4 months ago by jhc2.5k
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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 5 months ago by jhc2.5k
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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 5 months ago by jhc2.5k
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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 5 months ago by jhc2.5k
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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 5 months ago by jhc2.5k
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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 5 months ago by jhc2.5k

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Teacher 15 days ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar 22 days ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher 22 days 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 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: How Can I Plot Go Data Using R Or Any Tools?
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Scholar 5 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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Scholar 14 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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Scholar 19 months ago, created an answer that has been accepted. For A: Parsing Protein Trees to determine orthologs and paralogs
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