User: hyanwong

gravatar for hyanwong
hyanwong40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
4 months ago
Joined:
3 years, 11 months ago
Email:
h*******@googlemail.com

Posts by hyanwong

<prev • 20 results • page 1 of 2 • next >
1
vote
2
answers
329
views
2
answers
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 4 months ago by hyanwong40
1
vote
2
answers
329
views
2
answers
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 4 months ago by hyanwong40
0
votes
2
answers
329
views
2
answers
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 4 months ago by hyanwong40
0
votes
2
answers
329
views
2
answers
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 4 months ago by hyanwong40
2
votes
2
answers
329
views
2
answers
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 4 months ago by hyanwong40
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Plotting unrooted phylogenetic trees with anisometric collapsed nodes
... Thanks. Will check it out (also my misposted answer below) ...
written 2.9 years ago by hyanwong40
0
votes
1
answer
1.1k
views
1
answers
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 2.9 years ago by hyanwong40
0
votes
1
answer
1.1k
views
1
answers
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 2.9 years ago by hyanwong40
0
votes
1
answer
1.1k
views
1
answer
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 2.9 years ago by hyanwong40
0
votes
0
answers
1.7k
views
0
answers
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 3.3 years ago by hyanwong40

Latest awards to hyanwong

Scholar 4 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 2.9 years ago, created a question with more than 1,000 views. For Create genome annotation files for a personal genome
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Any good offline zoomable genome browsers?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Browser to display sequence searches in BAM files
Student 3.3 years ago, asked a question with at least 3 up-votes. For Any good offline zoomable genome browsers?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1978 users visited in the last hour