User: Sishuo Wang
Sishuo Wang • 130
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Posts by Sishuo Wang
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C: dN/dS analysis of genomes
... Maybe by setting mgene = in the control file? ...
written 7 days ago by
Sishuo Wang • 130
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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 7 days ago by
Sishuo Wang • 130
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C: Protein binding domain database
... Hi yuabrahamliu,
One way is to can try to collect all such domains, and search for them in databases like pfam, smart, etc. It might be time-consuming, though. ...
written 8 days ago by
Sishuo Wang • 130
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C: How to know the mm9 genome size?
... Would [FetchChromSizes][1] be helpful?
[1]: https://wiki.bits.vib.be/index.php/FetchChromSizes ...
written 8 days ago by
Sishuo Wang • 130
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... Hi,
I think to focus on the specific clades/lineages you are interested in is good. [This paper][1] and [this one][2] may be helpful to have a look.
Also, It seems to me that the distribution of all plant species might be too broad to do PAML positive selection analysis.
[1]: https://academic. ...
written 26 days ago by
Sishuo Wang • 130
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C: Swiss-Model vs. Modeller
... Both seem to me to be excellent tools, though you can always try [i-tasser][1] which has been in the 1st place in CASP for years.
[1]: https://zhanglab.ccmb.med.umich.edu/I-TASSER/ ...
written 4 weeks ago by
Sishuo Wang • 130
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... The following link may help you [link1][1], You can click on the tab "Sequences".
[1]: https://www.rcsb.org/pdb/static.do?p=download/web_download/download.jsp ...
written 5 weeks ago by
Sishuo Wang • 130
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Answer:
A: Error Running codeml
... Hi ammarsabir15,
In the second line of the control file, it is written as *treefile = tree.txt*. So, you may need to rename your tree file to "tree.txt" instead of "species.tree", and do the same thing for the alignment file ("seqfile.txt"). ...
written 5 weeks ago by
Sishuo Wang • 130
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... You can try [gblock][1] or [trimal][2]. Also, trees built using Maximum likelihood (available in MEGA5 I think) or Bayes methods instead of NJ might better reflect the evolutionary history of your sequences.
[1]: http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks
[2]: http://tr ...
written 5 weeks ago by
Sishuo Wang • 130
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Comment:
C: using NCBI SRA data for prinseq
... Exactly, it should perfectly work if you fix the problem of the line starting with the symbol "+". ...
written 5 weeks ago by
Sishuo Wang • 130
Latest awards to Sishuo Wang
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3.5 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)
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3.9 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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