User: Brice Sarver
Brice Sarver • 2.5k
- Reputation:
- 2,470
- Status:
- Trusted
- Location:
- United States
- Twitter:
- bricesarver
- Last seen:
- 1 year, 8 months ago
- Joined:
- 4 years, 1 month ago
- Email:
- b***********@gmail.com
I'm a postdoc currently working on mouse evolutionary genomics. I have a strong background in phylogenetics, genomics, molecular evolution, and phylogenomics. I use R, Python, and bash daily and act as a system administrator for servers dedicated to high-throughput sequencing analysis.
Posts by Brice Sarver
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Comment:
C: Why chip-seq is strand specific?
... How do you reconcile this answer with Devon's? ...
written 23 months ago by
Brice Sarver • 2.5k
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... Yes, though some models are only implemented in a Bayesian framework (e.g., UCLN vs. strict clock models in BEAST). Also, the default priors are a great starting point in modern approaches and generally perfectly acceptable for publication-worthy analyses. If you can construct informed priors, you s ...
written 23 months ago by
Brice Sarver • 2.5k
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... Are you specifying the root explicitly? Be aware that some visualizers select the root taxon arbitrarily. Do things look okay when you visualize the phylogeny as unrooted? ...
written 23 months ago by
Brice Sarver • 2.5k
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... If you're calibrating your phylogeny (placing priors on node ages), most Bayesian approaches work better than scaling after the fact. It's not fair to say one is better than the other; they produce different things with different assumptions about how to estimate the phylogeny in the first place. ...
written 23 months ago by
Brice Sarver • 2.5k
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... You'll want to do model selection on your dataset. Check out MrModelTest or DT-ModSel.
ML phylogenetics produces a point-estimate of the topology (the MLE). Bayesian methods, in addition to being able to specify priors on your analysis, produces a posterior distribution of trees. ...
written 23 months ago by
Brice Sarver • 2.5k
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... > However, in all articles I've seen, people try to build trees from complete orthogroups
Whether you use 'complete' orthogroups or not depends on the question you are trying to ask. It appears to just be a scale issue in your case. Your tree will still be representative of the relationships for ...
written 23 months ago by
Brice Sarver • 2.5k
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Answer:
A: Excel file Import to R
... I'm assuming you know what gene corresponds to each row. If they're in order, do something like:
a <- read.table("your_table_with_values.txt", stringsAsFactors=FALSE)
b <- [this is going to depend on what format your gene names are in.
perhaps you could read as a table and take a ...
written 24 months ago by
Brice Sarver • 2.5k
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... I think there is a lot of misunderstanding here. For starters:
1. Not all quantifying tools are based on mapping. Consider a distribution of per-base quality scores.
2. What is a non-experimental experiment?
3. Annotations can be derived experimentally or informatically. The latter is known to not ...
written 24 months ago by
Brice Sarver • 2.5k
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... You asked a similar question last week (https://www.biostars.org/p/217510/#217564), and my answer is the same. This looks to be a case of two different graphics combined. Check the differences in the fonts, for example. ...
written 24 months ago by
Brice Sarver • 2.5k
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... No control in what context? And what do you mean by control? For exome sequencing of clinical samples? ...
written 24 months ago by
Brice Sarver • 2.5k
Latest awards to Brice Sarver
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
24 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Is there any way to quantify differences between neighbour-joining phylogenetic
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: How to construct a tree with MEGA when some of the sequences are very short
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Voter
2.5 years ago,
voted more than 100 times.
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
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