User: johnnytam100

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johnnytam100100
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Posts by johnnytam100

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Why could we infer a physical time scale (e.g. a billion year) from a phylogenetic analysis?
... I have been wondering this question for a while: **Why could we infer a physical time scale (e.g. billion years) from a phylogenetic analysis?** or **What is the basis that we correlate the sequence similarity of two sequences with the time of evolution?** or **How do we deduce the physical tim ...
phylogeny phylogenetic tree written 10 months ago by johnnytam100100
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Comment: C: Statistics of amino acid usage of multiple aligned sequences?
... Yes, the input is an aligned .fasta file. ...
written 18 months ago by johnnytam100100
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Comment: C: Statistics of amino acid usage of multiple aligned sequences?
... I want to know, for each aligned position, the percentage of usage of amino acid species e.g. 80% A, 10% G, 10% V ...
written 18 months ago by johnnytam100100
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Statistics of amino acid usage of multiple aligned sequences?
... I would like to know if there is a tool which could do statistics of amino acid usage of multiple aligned sequences? I can do it in excel, just want to know if there is a tool conveniently do the job. Thanks! ...
alignment written 18 months ago by johnnytam100100 • updated 18 months ago by Joe17k
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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 21 months 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 21 months 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 21 months 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 21 months ago by johnnytam100100 • updated 21 months ago by zx87549.6k
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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 22 months 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 22 months ago by johnnytam100100

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