User: Brice Sarver
Brice Sarver • 2.5k
- Reputation:
- 2,520
- Status:
- Trusted
- Location:
- United States
- Twitter:
- bricesarve
- Last seen:
- 2 months, 1 week ago
- Joined:
- 4 years, 4 months ago
- Email:
- b***********@gmail.com
I'm a computational geneticist working in industry. My background is in phylogenetics, genomics, molecular evolution, and phylogenomics. I heavily utilize R, Python, bash, relational databases, and HPC Linux environments.
Posts by Brice Sarver
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... When I was in grad school, Geneious had a free version that could handle fasta sequences and primers. Looks like this isn't the case anymore. ...
written 11 weeks ago by
Brice Sarver • 2.5k
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... Have you tried downloading the [dbSNP VCF][1] from the NCBI FTP, then correlating that with your rsIDs?
Edit: I'm seeing GRCh37p13 and GRCh38p7 with a quick browse; 36 may be available in the archive.
[1]: https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ ...
written 11 weeks ago by
Brice Sarver • 2.5k
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Comment:
C: Large human disease datasets
... Could [GEO][1] be of use as a starting point? Search for 'human.'
[1]: https://www.ncbi.nlm.nih.gov/geo/ ...
written 11 weeks ago by
Brice Sarver • 2.5k
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... Have you considered [Geneious][1]?
[1]: https://www.geneious.com ...
written 11 weeks ago by
Brice Sarver • 2.5k
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... For a completely Python-based solution, I'd start with [DendroPy][1].
[1]: https://dendropy.org ...
written 11 weeks ago by
Brice Sarver • 2.5k
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... Why would a random starting tree not make sense? Sure, there could be better ones that are reasonable and fast to calculate (e.g., NJ), but this would just mean that the original tree is unlikely. Subsequent proposed changes to the topology (in a Bayesian or ML context) would be accepted via MCMC. P ...
written 11 weeks ago by
Brice Sarver • 2.5k
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... You're working with an alignment here, i.e., an inference of homology. As a result, there will be some underlying phylogenetic structure that you can infer which describes the relationships among the different lineages. You can also specify a model of sequence evolution that will inform your analysi ...
written 3 months ago by
Brice Sarver • 2.5k
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1.4k
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Comment:
C: Why chip-seq is strand specific?
... How do you reconcile this answer with Devon's? ...
written 2.2 years 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 2.2 years ago by
Brice Sarver • 2.5k
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788
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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 2.2 years ago by
Brice Sarver • 2.5k
Latest awards to Brice Sarver
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: Software for evaluating multiple sequence alignments before phylogenetic analysi
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Quickly subsetting VCF while being memory efficient
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: The nucleotides on ENST00000347310 and ENST00000425614 do not agree on the same
Good Answer
23 months ago,
created an answer that was upvoted at least 5 times.
For A: trimming fastq files with Trimmomatic
Teacher
23 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
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Identifying degenerate positions in Mus
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: trimming fastq files with Trimmomatic
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
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
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.3 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: Is there any way to quantify differences between neighbour-joining phylogenetic
Teacher
2.3 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
2.3 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.3 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
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
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