similar to: Skyline plots from several trees in newick format

Dear all, Does anyone know how can one loop through the newick phylogenetic trees stored in a nexus file and generate an "average" skyline plot with coalescent intervals? I have managed to generate the plot with one tree, but is it possible to create that "consensus/average" plot in R? tr<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1,

Hi, I have generated a skyline plot of a tree in newick format using "ape". How can I plot the error bars for this graph? I only have the the tree data. un<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (((((15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0,

Hi All, Just 10 days after 3.0.7 we''re releasing 3.0.8 with support for SQLite3. In combination with our demo application, this makes trying out Skyline CMS a breeze. We also enabled Github issues for Skyline to track bugs and issues with Skyline CMS. Besides the SQLite3 support the most notable change since 3.0.7 is the improved API documentation which you can find on

https://bugzilla.samba.org/show_bug.cgi?id=5008 Summary: make check fails on Cygwin (default-acls) Product: rsync Version: 3.0.0 Platform: x86 OS/Version: Other Status: NEW Severity: normal Priority: P3 Component: core AssignedTo: wayned@samba.org ReportedBy: Denis.Excoffier@airbus.com

Mates, I'm trying to solve some log errors I getting. I have samba 3.0.7 installed on Suse 9.0. It has been happening intermittently for several months. I don't know if this is XP client related or what. Any thoughts: The errors are: Feb 9 20:00:33 skyline smbd[14408]: [2005/02/09 20:00:33, 0] lib/util_sock.c:get_peer_addr(1000) Feb 9 20:00:33 skyline smbd[14408]: getpeername

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear R-helpers, I would like to export hierarchical clusters e.g. fit <- hclust(d, method="ward") in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package.

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

Andrew, Jerry and the rest of the team: Hello again! It has been quite some time since I was here and waded the waters to set up bind8 and samba 2.07 on my trust mdk 7.2 box. (by the way, it is still working like a champ) over 400 days uptime before the last extended power outage. Well, obviously a lot has changed since the 2.07 days and I am now working on a SuSE 8.2 box with samba 2.2.7a

Not sure if this got through the 1st time, so I am trying a repost. I appologize if you get this twice, but I need help! -- David C. Rankin, J.D., P.E. Rankin * Bertin, PLLC 510 Ochiltree Street Nacogdoches, Texas 75961 (936) 715-9333 (936) 715-9339 fax www.rankin-bertin.com -- ----- Original Message ----- From: "David Rankin" <drankin@cox-internet.com> To: "samba"

Hello, I am trying to run some AMOVA analyses with the amova function in the package ade4. When running the example dataset provided in ade4, I noticed a difference between the published results from the same data (Excoffier et al. 1992) and what ade4 calculates. Below are the data for "within sample/population" from ade4 and from the haplotypic distance matrix in the paper:

Mates, On my Suse 9.0 pro installation, I updated Samba from 2.2.8a to 3.0.7. The upgrade went flawlessly, Samba is happily sharing all the files it was before. However, I can no longer print via cups. I have a HP LJ4 attached to the Linux box that worked great before the upgrade. I have 2 XP clients. Now from the Windows side, I get the printer status showing 'access denied, unable to

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

This isn't necessarily a samba problem, but its happening on my domain with a Samba PDC. I have 2 computers running XP Pro that I can only connect to intermittently. All 3 of these machines are joined to the domain and can access domain resources when logged in as a domain user through the Samba PDC. SHIPPING1 always seems to work. SHOP1 and SHOP2 are the ones that allow intermittent

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Hi, I've been investigating the ape package for a while, and I was wondering if it is possible to: - display the names of the internal nodes (from a newick tree) - plot a pie-chart on top of each of the internal branches in a phylogram plot Thanks in advance, Cheers, Albert.

Hi all, I'm on Mac OS X 10.4... So I've got a small python script I need to run from R. However, to get the python script working, I need to have the shell that R calls get settings from my .bash_profile file, which apparently it doesn't currently (the shell R calls uses an older version of python, and also this older version of python can't see various python modules I have

Greetings, I have tried a few days on an off to get samba to work, but need some help. Samba version Samba 3.0.23a-1.FC5.1 Linux Fedora 5 (localhost) User: dsmith 192.168.1.104 Windows XP SP2 with lastest updates (T2385) User: dan 192.168.1.100 Linksys 8 port router I found a couple problems with the checklist and fixed them. A couple problems I wasn't able to solve. Here are the

There was talk a few weeks ago about the possibility of a Tk-based user management tool that never happened. I'm planning on trying to do this myself. What features were to be in the one that never materialized? What features might people want in it? To begin, the program will only be able to do things that can be done straight through the existing command line tools (net, smbpasswd,

I don't know the final answer BUT if you have something simmilar to a cyber-cafe LAN (I mean, users use all the computers, and maybe some users come back to login with the same name) then you have to install a printer only once in a computer, loging as the administrator and installing drivers. Then what users will have to do is JUST add the printer without installing. I know that it's