User: DNAngel
DNAngel • 30
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- 30
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- New User
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- Last seen:
- 7 hours ago
- Joined:
- 2 years, 4 months ago
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- k********************@hotmail.com
Posts by DNAngel
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... I was wondering if there are any R packages or tools that can determine the evolutionary rates of species given their tree (with branch lengths) and an alignment file for a specific gene. I want to see if some species belonging to a clade are evolving more quickly than the ancestral clades.
Is this ...
written 12 days ago by
DNAngel • 30
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... Hello,
I was wondering if anyone knew of a program or R package that calculates ancestral character states of discrete traits (i.e. habitat, skin colour) using maximum parsimony? The ape package utilizes models that are all likelihood based. I want to implement both methods and compare the results ...
written 3 months ago by
DNAngel • 30
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... I have many multiple sequence alignments containing protein-coding genes aligned by codons and I want to generate pairwise similarity tables between each pair of sequences. I know Geneious used to do this but I no longer have it on trial nor can I afford to buy it. ...
written 3 months ago by
DNAngel • 30
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... Hi all,
This might be a noob question but I was just wondering, what does it mean if an internal branch has a higher dN/dS ratio but the tips leading from that branch have low dN/dS values. I ran the M0 model for a gene just to test things and understand the output data.
Here's an example of what ...
written 4 months ago by
DNAngel • 30
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... Okay I can try the free ratio model as well, but I don't think it gives me individual dN and dS values with their individual branch lengths. I have to make a dN and dS tree where I can use their individual branch lengths and compare the differences visually in that manner. M0 gives individual dN and ...
written 4 months ago by
DNAngel • 30
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... Also, why would model M1a be used to check for branch-specific dN and dS? Why not model M0 which doesn't constrain it since M1a does not allow positive selection anyways? ...
written 4 months ago by
DNAngel • 30
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... I am confused still, if there are 2000 N and only 650 S, how is the overall dN/dS less than 1? ...
written 4 months ago by
DNAngel • 30
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... Hi all,
Could someone just clarify the following output for me?
Example output:
branch t N S dN/dS dN dS N*dN S*dS
38..1 0.431 2257.5 655.5 0.0546 0.0294 0.5379 66.3 352.6
38..39 0.068 2257.5 655.5 0.0546 0.0046 0.0843 10. ...
written 4 months ago by
DNAngel • 30
• updated
4 months ago by
Dave Carlson • 90
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... I have exome sequencing data and as far as I know, it should include all exonic regions including the mitochondrial genome. When I blast my sequences to recover mitochondrial protein-coding genes, I get a ton of intermittent stop codons and a lot of gaps which I generally do not find when extracting ...
written 4 months ago by
DNAngel • 30
• updated
4 months ago by
Jeremy Leipzig ♦ 18k
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... How would I use Blast+ if my organisms don't have references or have the genes sequenced previously?? The reference species exists on ensembl so would that be an option? I do have a lot of reads, each species has over 1 million single-end reads. ...
written 5 months ago by
DNAngel • 30
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