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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... 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 18 days 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 22 days 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 5 weeks 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 weeks 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 weeks ago by
Sishuo Wang • 140
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C: dN/dS analysis of genomes
... I think that should work. ...
written 8 weeks 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 8 weeks ago by
Sishuo Wang • 140
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Comment:
C: dN/dS analysis of genomes
... Hi Mehmet,
Sorry, not sure.
Have you got anything in the mlc file? Or was the analysis disrupted?
By the way, there was a typo in "eqfile = all.paml". ...
written 8 weeks ago by
Sishuo Wang • 140
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Comment:
C: dN/dS analysis of genomes
... Maybe by setting mgene = in the control file? ...
written 10 weeks ago by
Sishuo Wang • 140
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Comment:
C: dN/dS analysis of genomes
... Hi Mehmet,
I think calculating dn/ds per alignment is good. You can create quick trees for the alignment as input of codeml, otherwise you could let the programme do it. ...
written 10 weeks ago by
Sishuo Wang • 140
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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)
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4.1 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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