User: Sishuo Wang
Sishuo Wang • 140
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- The University of British Columbia
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Posts by Sishuo Wang
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... Have a try of the pubmedy add-in in chrome and you will see the number of citations as
![enter image description here][1]
[1]: https://www.novoprolabs.com/images/2017121915136672881056.png ...
written 7 weeks ago by
Sishuo Wang • 140
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... You can have a look at [this][1]. Alternatively, you may wish to try [UGENE][2] for removing gaps. For other characters, it might be possible to convert them into '-' first?
[1]: https://stackoverflow.com/questions/28220301/python-remove-special-column-from-multiple-sequence-alignment
[2]: htt ...
written 9 weeks ago by
Sishuo Wang • 140
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... should be included in *.faa ...
written 12 weeks ago by
Sishuo Wang • 140
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... Hi,
I think [seqret][1] from EMBOSS can do the job. You can set the [output format][2] as clustal.
[1]: https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/
[2]: https://www.ebi.ac.uk/seqdb/confluence/display/THD/EMBOSS+seqret#EMBOSSseqret-sequence ...
written 4 months ago by
Sishuo Wang • 140
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... [exonerate][1] may be a good option.
[1]: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-user-guide ...
written 4 months ago by
Sishuo Wang • 140
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... You can try [orthofinder][1] or [get_homologues][2] instead for gene family clustering or identification of orthologs. Neither of them needs mysql connection.
[1]: https://github.com/davidemms/OrthoFinder
[2]: http://aem.asm.org/content/79/24/7696.full ...
written 4 months ago by
Sishuo Wang • 140
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Comment:
C: Orthofinder: orthogroup graph
... It seems that the author of orthofinder does not suggest changing the inflation index.
[link][1]
[1]: https://github.com/davidemms/OrthoFinder/issues/34 ...
written 5 months ago by
Sishuo Wang • 140
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Comment:
A: How I can find flanking regions
... Hi, You may feel bedtools flank ([link][1]) helpful,
[1]: http://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 5 months ago by
Sishuo Wang • 140
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Comment:
C: dN/dS analysis of genomes
... I think that should work. ...
written 5 months ago by
Sishuo Wang • 140
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... Hi Shred,
Maybe you can try the tools introduced by [this paper][1]. You can find the scripts in the supplemental files.
[1]: https://academic.oup.com/gbe/article/7/12/3416/2467318 ...
written 5 months ago by
Sishuo Wang • 140
Latest awards to Sishuo Wang
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4.0 years ago,
created a question with more than 1,000 views.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
Student
4.4 years ago,
asked a question with at least 3 up-votes.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
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