User: hyanwong

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hyanwong40
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40
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New User
Location:
United Kingdom
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4 weeks ago
Joined:
3 years, 8 months ago
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h*******@googlemail.com

Posts by hyanwong

<prev • 20 results • page 1 of 2 • next >
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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 28 days ago by hyanwong40
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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 28 days ago by hyanwong40
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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 29 days ago by hyanwong40
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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 29 days ago by hyanwong40
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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 29 days ago by hyanwong40
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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 2.7 years ago by hyanwong40
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Answer: A: Plotting unrooted phylogenetic trees with anisometric collapsed nodes
... (Sorry - in reply to h.mon's comment above). Ah, I hadn't investigated that. Thanks. Meanwhile I managed to hack ARB to work on my mac, so I have a nice universal tree of life now, which was my aim ...
written 2.7 years ago by hyanwong40
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Comment: C: Plotting unrooted phylogenetic trees with anisometric collapsed nodes
... Thanks. But as far as I can tell it doesn't work on unrooted tree displays, unfortunately. And even on rooted ones, the collapsed triangles are isometric. ...
written 2.7 years ago by hyanwong40
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Plotting unrooted phylogenetic trees with anisometric collapsed nodes
... I want to draw an unrooted tree for a publication, and be able to drag the nodes around. There's lots of software that will do that. But I also want to collapse subtrees down into a triangle shape, and have the lengths of sides of the triangle correspond to the shortest and longest branches in the s ...
software phylogenetics visualization written 2.7 years ago by hyanwong40
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Comment: C: Create genome annotation files for a personal genome
... Cheers. So if I can't do this easily with an arbitrary personal genome, is there any way to display e.g. extra opsin repeats, or possible locations of Epstein-Barr (which as I understand isn't in the reference seq) in well-known genomes such as James Watson, or Venter's HuRef? ...
written 3.1 years ago by hyanwong40

Latest awards to hyanwong

Scholar 28 days 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 2.6 years ago, created a question with more than 1,000 views. For Create genome annotation files for a personal genome
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Any good offline zoomable genome browsers?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Browser to display sequence searches in BAM files
Student 3.1 years ago, asked a question with at least 3 up-votes. For Any good offline zoomable genome browsers?

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