User: hyanwong

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hyanwong60
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United Kingdom
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Posts by hyanwong

<prev • 24 results • page 1 of 3 • next >
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Where to save metadata about trees in a nexus file?
... I have a large set of trees in a nexus file, and want to associate a weighting with each tree. Where in the nexus format can I store this sort of per-tree metadata? I've looked at http://informatics.nescent.org/w/images/8/8b/NEXUS_Final.pdf and can't see anything obvious, but I think I must be missi ...
nexus tree written 16 days ago by hyanwong60
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Conventions for sorting provenance (original URL, processing steps) in VCF file
... I'm creating a set of VCFs, one for each human chromosome, by taking a single VCF from e.g. ftp://ftp.ensembl.org/pub/release-91/variation/vcf/homo_sapiens/homo_sapiens.vcf.gz and running bcftools view homo_sapiens.vcf.gz --regions 1 -Oz -o homo_sapiens_chr1.vcf.gz I would like to store in eac ...
vcf metadata provenance written 10 weeks ago by hyanwong60
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Comment: C: Why might ancestral allele states in 1000G be wrong?
... Yes, although from what I’ve read, dbSNP only uses the chimp sequence as the ancestral state, which is much less sophisticated than the 1000G method. I wondered if either the alignments for this region with other species have improved since the 100G calculation, or if there’s a bug in the 1000G AA e ...
written 5 months ago by hyanwong60
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Why might ancestral allele states in 1000G be wrong?
... According to ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README ancestral alleles in the human SNPs in 1000 genomes data are determined by comparison with chimp, orangutan, and macaque. Here's an example from the vcf for chromosome 1 (e.g. from http:/ ...
1000 genomes ancestral alleles written 5 months ago by hyanwong60 • updated 4 months ago by Jie Ping20
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Comment: C: How to root a tree in R with a polytomy at the root
... Cheers. Always good to get advice from the author of the library :) ...
written 10 months ago by hyanwong60
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Answer: A: How to root a tree in R with a polytomy at the root
... Emmanuel Paradis has pointed out that the solution is simple - the tree is treated as unrooted because the deepest node has no length. So all I have to do is to place ":0" before the terminal semicolon, and the tree should be treated as rooted. ...
written 10 months ago by hyanwong60
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Comment: C: How to root a tree in R with a polytomy at the root
... Does that maintain the polytomy? I.e. is this the same tree as if it were rooted at 2? From a casual inspection it seems not: > t1 = read.tree(text="[&R] (1:1.250,2:1.250,(3:0.750,(4:0.500,5:0.500):0.250):0.500);") > t2 <- root(t1, outgroup=1, resolve.root=TRUE) > t3 < ...
written 10 months ago by hyanwong60
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Comment: C: How to root a tree in R with a polytomy at the root
... I want to compare this tree with an alternative (in this example, strictly bifurcating) tree, as (1:0.833,(2:0.225,(3:0.209,(4:0.114,5:0.114):0.095):0.016):0.608);, and calculate distance metrics between them. This is not strictly defined for some common stats, such as the Robinson-Foulds distance, ...
written 10 months ago by hyanwong60
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How to root a tree in R with a polytomy at the root
... In R, I have a phylogenetic tree like this, with a polytomy at the root: library(ape) t1 = read.tree(text="[&R] (1:1.250,2:1.250,(3:0.750,(4:0.500,5:0.500):0.250):0.500);") But it is treated as unrooted: > is.rooted(t1) [1] FALSE How can I force it to be rooted at the poly ...
R phylogenetics written 10 months ago by hyanwong60
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Comment: C: Plotting unrooted phylogenetic trees with anisometric collapsed nodes
... Thanks. Will check it out (also my misposted answer below) ...
written 3.4 years ago by hyanwong60

Latest awards to hyanwong

Popular Question 10 months ago, created a question with more than 1,000 views. For Plotting unrooted phylogenetic trees with anisometric collapsed nodes
Scholar 10 months ago, created an answer that has been accepted. For A: How to root a tree in R with a polytomy at the root
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Create genome annotation files for a personal genome
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Any good offline zoomable genome browsers?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Browser to display sequence searches in BAM files
Student 3.8 years ago, asked a question with at least 3 up-votes. For Any good offline zoomable genome browsers?

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