User: prfsullivan

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Posts by prfsullivan

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Comment: C: Use PCoA plot rather than phylogenetic tree?
... To add a bit more perspective on the second reason -- I work in field where we isolate secondary metabolites to identify drug leads. Highly related organisms (species, more or less) tend to produce the same chemistry. More distantly related strains generally do not. Thus, I only really care if st ...
written 5 weeks ago by prfsullivan0
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Thanks for the reply. Reasons I want a 2D non-hierarchical vsuaization: 1) I've found when using the 16S sequence (750 bp length), branches between two distant clades tend to have low bootstrap support. Thus, clear hierarchical relationships are often difficult to establish. 2) I'm only looki ...
written 5 weeks ago by prfsullivan0
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Yeah, I'm a little concerned that I can't do that. One suggestion I heard to was to bin the sequences into OTUs and then run a beta-diversity analysis. Is there no tool available to assess phylogenetic relationships in a 2D plot? I've read about multidimensional scaling, which might be what I'm ...
written 5 weeks ago by prfsullivan0
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Thanks for the reply. I haven't been able to find a reference paper doing something similar but will keep looking. The 10k sequences is after redundant sequence removal. I have a global dataset of 10,000 sequences. Of the 10,000, there are 300 sequences (strains) that I am looking to highlig ...
written 5 weeks ago by prfsullivan0
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Comment: C: Program to plot 60,000 16S rRNA dataset for phylogenetic assessment?
... Yeah I realized that I do not want to do a beta diversity analysis. I'm basically looking to analyze a small subset's phylogenetic relatedness amongst each other compared to a global population. I essentially want to run a standard phylogenetic analysis (maximum likelihood method, most likely) ...
written 5 weeks ago by prfsullivan0
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Ok, updated the post. ...
written 5 weeks ago by prfsullivan0
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Use PCoA plot rather than phylogenetic tree?
... Hello, I have a large dataset (>10,000) of 16S rRNA sequences. Rather than build a phylogenetic tree, I'd rather visualize the analysis on a 2D PCoA-like plot. I plan to use a maximum likelihood method for the analysis and ultimately want to portray the data in a PCoA-like plot. Tree topolo ...
gene written 5 weeks ago by prfsullivan0 • updated 5 weeks ago by h.mon31k
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(Closed) Program to run analysis of 60,000 16S sequences?
... Hello, I have a huge dataset with 60,000 16S sequences -- this total number will drop once redundant sequences are removed. Rather than building a phylogenetic tree, I am looking to run a phylogenetic analysis and ultimately plot the output. I do not care about the dataset's topology. I just want ...
gene software error written 5 weeks ago by prfsullivan0
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Comment: C: Program to plot 60,000 16S rRNA dataset for phylogenetic assessment?
... The length would be ~1,000 bp. I was planning to get rid of redundancy so I'd reduce the sample size but my guess is the dataset would still 10,000-20,000. ...
written 6 weeks ago by prfsullivan0
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Program to plot 60,000 16S rRNA dataset for phylogenetic assessment?
... Hello, I'm looking to do a large-scale phylogenetic analysis. I plan to build a PCA plot with 60,000+ DNA sequences. I'd be doing a beta-diversity analysis with one sample comprised of 60,000 sequences while the other three are <200 sequences. I want all of the individual sequences to be inclu ...
gene written 6 weeks ago by prfsullivan0 • updated 5 weeks ago by h.mon31k

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