User: Brice Sarver
Brice Sarver • 2.5k
- 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
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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 Sarver • 2.5k
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... Are you sure you really want a phylogeny and not simply a dendrogram from, say, hierarchical clustering? ...
written 23 days ago by
Brice Sarver • 2.5k
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... 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 Sarver • 2.5k
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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 Sarver • 2.5k
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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 4 months 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 4 months 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 4 months ago by
Brice Sarver • 2.5k
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315
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... Have you considered [Geneious][1]?
[1]: https://www.geneious.com ...
written 4 months 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 4 months 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 4 months ago by
Brice Sarver • 2.5k
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
Appreciated
2.1 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
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
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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