User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

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Comment: C: Nexus file in Beast
... You should be able to import a nexus file into BEAUti relatively easy. You can then make a configuration file in the xml format from there. ...
written 18 days ago by Giovanni.madrigal12170
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Comment: C: Looking for an annotation-aware sequence alignment visualization tool
... [IGV][1]? [1]: http://software.broadinstitute.org/software/igv/book/export/html/6 ...
written 3 months ago by Giovanni.madrigal12170
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Comment: C: How to use beast on sequence data with time?
... For questions pertaining to beast, I highly recommend going to their google group [here][1] and seeing if your question has already been answered or if needed, you can open up a new topic. Regarding your questions, I can try to answer your questions but take them with a grain of salt since I am not ...
written 4 months ago by Giovanni.madrigal12170
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Comment: C: Sorting BLAST file
... Are you sure your e-value is in column 10? ...
written 4 months ago by Giovanni.madrigal12170
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Answer: C: Sorting BLAST file
... Ah, is your file space delimited? If so, try this awk -F ' ' '{if ($10 <= 0.001) print $0}' blast_file.txt > Filtered_blast_file.txt ...
written 4 months ago by Giovanni.madrigal12170
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Comment: A: Sorting BLAST file
... If selecting for evalues below, let's say 0.001 and assuming your file is tab delimited, awk -F '\t' '{if ($10 <= 0.001) print $0}' blast_file.txt > Filtered_blast_file.txt ...
written 4 months ago by Giovanni.madrigal12170
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Comment: C: Blast: use best hit or top20 hits?
... I agree with this. If I am correct, BLAST2GO has several filtering steps for blast hits (e.g. Blast Description Annotator (BDA)) that help you narrow down to the "best" hits. ...
written 5 months ago by Giovanni.madrigal12170
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Answer: A: Searching for GO terms
... [BioMart][1] is a pretty useful tool with a couple of ways of mining for GO information. [1]: https://m.ensembl.org/info/data/biomart/index.html ...
written 5 months ago by Giovanni.madrigal12170
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Comment: C: How to upgrade R version in ubuntu?
... I'm not quite sure what the error would be. If you followed all the instructions, it should have worked. ...
written 10 months ago by Giovanni.madrigal12170
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Comment: C: How to upgrade R version in ubuntu?
... What does your source.list look like? ...
written 10 months ago by Giovanni.madrigal12170

Latest awards to Giovanni.madrigal12

Scholar 4 months ago, created an answer that has been accepted. For C: Sorting BLAST file
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: STRUCTURE software file format

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