User: Sishuo Wang

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Sishuo Wang140
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Posts by Sishuo Wang

<prev • 46 results • page 1 of 5 • next >
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Comment: C: File format conversion to clustal using biopython
... 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 Wang140
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Comment: C: tools to align DNA sequences against protein sequence
... [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 Wang140
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Comment: C: OrthoMCL problem when connecting with mysql
... 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 Wang140
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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 Wang140
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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 Wang140
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Comment: C: dN/dS analysis of genomes
... I think that should work. ...
written 8 weeks ago by Sishuo Wang140
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Comment: C: Find all sequence of a specific genus amplified by a couple of primers
... 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 Wang140
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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 Wang140
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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 Wang140
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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 Wang140

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