User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver2.4k
Reputation:
2,380
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Location:
United States
Twitter:
bricesarver
Last seen:
11 months, 2 weeks ago
Joined:
3 years, 4 months 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

<prev • 256 results • page 1 of 26 • next >
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Comment: C: Why chip-seq is strand specific?
... How do you reconcile this answer with Devon's? ...
written 14 months ago by Brice Sarver2.4k
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Comment: C: Phylogenetic tree using ML algorithm
... 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 14 months ago by Brice Sarver2.4k
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Comment: C: Weird phylogenetic tree (bacterial transporters)
... 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 14 months ago by Brice Sarver2.4k
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Comment: C: Phylogenetic tree using ML algorithm
... 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 14 months ago by Brice Sarver2.4k
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Answer: A: Phylogenetic tree using ML algorithm
... 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 14 months ago by Brice Sarver2.4k
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Answer: A: Phylogeny from incomplete orthogroups
... > 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 14 months ago by Brice Sarver2.4k
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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 14 months ago by Brice Sarver2.4k
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Comment: C: Please, please, define what a 'read' is.
... 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 14 months ago by Brice Sarver2.4k
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Answer: A: How to draw a phylogenetic tree together with a genome locus structure?
... 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 15 months ago by Brice Sarver2.4k
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Comment: C: burden test/SKAT on exome study without control
... No control in what context? And what do you mean by control? For exome sequencing of clinical samples? ...
written 15 months ago by Brice Sarver2.4k

Latest awards to Brice Sarver

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 15 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 15 months ago, created an answer that has been accepted. For A: Is there any way to quantify differences between neighbour-joining phylogenetic
Scholar 15 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 15 months 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 15 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 15 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 16 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 16 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 16 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 17 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 18 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Voter 21 months ago, voted more than 100 times.
Scholar 23 months ago, created an answer that has been accepted. For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Teacher 24 months 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 24 months ago, created an answer that has been accepted. For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Scholar 24 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 2.0 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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