User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver2.5k
Reputation:
2,540
Status:
Trusted
Location:
United States
Twitter:
bricesarve
Last seen:
2 days, 7 hours ago
Joined:
4 years, 6 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 • 267 results • page 1 of 27 • next >
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Comment: C: paired reads have different names
... Agreed. mm, please provide the BWA call. One input FASTQ or two? ...
written 23 days ago by Brice Sarver2.5k
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Comment: C: Distance based tree reconstruction
... Are you sure you really want a phylogeny and not simply a dendrogram from, say, hierarchical clustering? ...
written 23 days ago by Brice Sarver2.5k
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Answer: A: Multigene-Phylogeny: How to merge several Multiple-Sequence-Alignments?
... I provided this solution for another question, but it will work just as well for combining MSAs: https://www.biostars.org/p/365602/#365697 ...
written 23 days ago by Brice Sarver2.5k
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Answer: A: merge two multifasta files
... Here's a quick R solution using Bioconductor. There are analogous examples using a variety of different tools and languages (see Biopython, etc.). For quick manipulations, I like to use Biostrings due to how efficiently it handles long strings once in memory. library(Biostrings) a <- rea ...
written 23 days ago by Brice Sarver2.5k
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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 4 months 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 4 months 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 4 months 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 4 months 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 4 months 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 4 months ago by Brice Sarver2.5k

Latest awards to Brice Sarver

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 4 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
Scholar 4 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: trimming fastq files with Trimmomatic
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: The nucleotides on ENST00000347310 and ENST00000425614 do not agree on the same
Teacher 2.1 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 2.1 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Appreciated 2.1 years 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: Software for evaluating multiple sequence alignments before phylogenetic analysi
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Identifying degenerate positions in Mus
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: split supermatrix by gene
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Quickly subsetting VCF while being memory efficient
Teacher 2.3 years ago, created an answer with at least 3 up-votes. 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
Teacher 2.4 years ago, created an answer with at least 3 up-votes. 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: Is there any way to quantify differences between neighbour-joining phylogenetic
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: How to construct a tree with MEGA when some of the sequences are very short
Scholar 2.4 years ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 2.5 years ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree

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