User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver2.5k
Reputation:
2,520
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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

<prev • 263 results • page 1 of 27 • next >
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Comment: C: tool for genome sequence manipulation
... 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 Sarver2.5k
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Answer: A: SNP coordinates for all genome builds
... 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 Sarver2.5k
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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 Sarver2.5k
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Answer: A: tool for genome sequence manipulation
... Have you considered [Geneious][1]? [1]: https://www.geneious.com ...
written 11 weeks ago by Brice Sarver2.5k
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Answer: A: Reconstruction of a generic tree using dynamic data with python
... For a completely Python-based solution, I'd start with [DendroPy][1]. [1]: https://dendropy.org ...
written 11 weeks ago by Brice Sarver2.5k
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Comment: C: Reconstruction of a generic tree using dynamic data with python
... 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 Sarver2.5k
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Answer: A: Working Principle of Ancestral Sequence Reconstruction (ASR)
... 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 Sarver2.5k
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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 Sarver2.5k
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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 2.2 years ago by Brice Sarver2.5k
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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 2.2 years ago by Brice Sarver2.5k

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
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: split supermatrix by gene
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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