User: weedy23

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weedy2370
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Posts by weedy23

<prev • 6 results • page 1 of 1 • next >
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Advice on publishing maximum likelihood trees
... Hi, I am relatively new to phylogenetic analyses so I have a simple question. I have done a multi-species maximum likelihood analysis in Garli. I have obtained a "best" tree in Garli from multiple runs. I then conducted a bootstrap analysis (1000 replicates) and imported the 1000 bootstrap trees in ...
phylogenetics maximum likelihood sequencing written 5 months ago by weedy2370
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Comment: C: Obtain one vcf file of shared SNPs from input files with different samples using
... Hi, sorry I only just saw your comment. I ended up using vcf-merge instead. However, it included ALL loci in the output file, not just loci present in all the files. So I had to go through the output file and delete all the loci that were missing for one or more of the populations. Not ideal but it ...
written 3.4 years ago by weedy2370
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Can't explain AMOVA result
... Hi there, I am hoping that someone can help me explain this result I got when conducting an AMOVA analysis on SNP data in Arlequin. I understand the test and have used AMOVA before but this result has me confused. I am testing 3 populations, 2 which are grouped together. The two grouped populations ...
arlequin amova snp population genetics written 3.4 years ago by weedy2370 • updated 3.0 years ago by pvrandsoe0
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Comment: C: Obtain one vcf file of shared SNPs from input files with different samples using
... Yep exactly. ...
written 3.7 years ago by weedy2370
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Comment: C: Obtain one vcf file of shared SNPs from input files with different samples using
... Hi venu, thanks for your help. The vcf-isec code you wrote is basically what I did, but I just specified exactly 3 files rather than 3 or more, and an uncompressed output instead. However, this gave me a file with only the individuals in the first file in it (although it did give me the loci found o ...
written 3.7 years ago by weedy2370
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Obtain one vcf file of shared SNPs from input files with different samples using vcf-isec (vcftools)
... I am new to Linux and programming and am trying to use vcftools. I have 3 vcf files; each one is a different population (i.e. with no shared individuals between the files). I am trying to use vcf-isec to merge the 3 files and end up with one vcf file that contains only the SNPs that are present in a ...
vcf vcftools written 3.7 years ago by weedy2370 • updated 3.7 years ago by venu6.3k

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For Can't explain AMOVA result

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