User: johnnytam100

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johnnytam100100
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Posts by johnnytam100

<prev • 70 results • page 1 of 7 • next >
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Extracting sequence names from phylogenetic tree (in newick format or MEGA)?
... I would like to extract the sequence names of a certain node of a phylogenetic tree built in MEGA. Since there are quite a lot of sequence of the node (up to thousand), is there a method to extract the sequence names by specifying a node either using the newick format or MEGA? Thanks! ...
phylogenetic tree written 6 weeks ago by johnnytam100100
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Comment: C: R: scaling axis for different limits in hist
... Sorry for confusing by the term I used. The "physical lengths" means the height of the axis. ...
written 6 weeks ago by johnnytam100100
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Comment: C: R: scaling axis for different limits in hist
... Thanks Wouter! I will post on stackoverflow next time. ...
written 6 weeks ago by johnnytam100100
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R: scaling axis for different limits in hist
... I am plotting several frequency plots using `hist` in R. For different plots, there is a different maximum value for the y-axis, e.g. Plot 1:15000 as max Plot 2: 80000 as max However, as a different limit of the axis was set, the physical lengths of the y-axes of the two graphs were different ...
R hist written 6 weeks ago by johnnytam100100 • updated 6 weeks ago by zx87546.2k
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Comment: C: How do we call this phenomenon in evolution?
... Yes, that's much related. I have just read from a reference book, "co-evolving residues". Please throw in more specific terms or examples describing such a phenomenon if anyone has. ...
written 7 weeks ago by johnnytam100100
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How do we call this phenomenon in evolution?
... I have a protein of interest, which is conserved from bacteria, archaea to eukaryotes. After aligning the sequence a highly conserved domain of the homologs, I have divided the sequences into three groups which differ by a significant number of the aligned position that shared a common trend, in te ...
evolution written 7 weeks ago by johnnytam100100
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Comment: C: How to query taxonomy ID using protein accession ID in NCBI or Uniprot?
... Solved. Download from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ as suggested by Sej Modha [here][1] [1]: https://www.biostars.org/p/276817/#280743 ...
written 9 weeks ago by johnnytam100100
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How to query taxonomy ID using protein accession ID in NCBI or Uniprot?
... I want to query a list of taxonomy ID of the proteins using a list of the protein accession ID in NCBI or Uniprot. Does NCBI or Uniprot provide a file which correlates the taxonomy ID, protein accession ID etc. in a table format? Thank you! ...
ncbi taxonomy uniprot written 9 weeks ago by johnnytam100100
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Comment: C: How could we compare the extent of evolution between two species?
... Inspiring! I feel exactly the same here that I am mixing up things... If I rephrase my question into a purely technical question: is there a pre-built phylogenetic tree for 16s RNA for all sequenced species? ...
written 9 weeks ago by johnnytam100100
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Comment: C: What is the standard way of preparing homolog sequences for a phylogenetic analy
... For the outgroup, should it be either 'out' in the sense of 1) blast threshold 2) functional annotation of the protein or 3) both? ...
written 9 weeks ago by johnnytam100100

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Student 12 weeks ago, asked a question with at least 3 up-votes. For So frustrated compiling necessary packages in a linux system

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