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Questions tagged [ape]

APE is a full-featured open source solution designed for Ajax push. It includes a webserver and a JavaScript framework. APE allows to implement any kind of real-time data streaming to a web browser, without having to install anything on the client-side.

Ajax Push Engine (APE) is a full-featured open source solution designed for Ajax push. It includes a webserver and a JavaScript framework. APE allows to implement any kind of real-time data streaming to a web browser, without having to install anything on the client-side.

APE project: http://www.ape-project.org Related: http://en.wikipedia.org/wiki/Comet_(programming)‎ also: http://ajaxpatterns.org/HTTP_Streaming

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Can't contact Ape-Server on VM from Host

i just want to use APE on my local computer. It's my first time i installed APE on a virtual machine running ubuntu and i tested it in the VM with the check-tool on local.ape-project.org/APE_JSF/Tools/Check/ successfully. I got happily the bold…
kuro
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Having trouble performing mantel test with assymetrical matrices

I am trying to compare distances matrices belonging to two species matrices. One is bacteria and the other is ectomycorrhizal fungi. Both species matrices were generated from the same plant roots using different extraction methods. I want to compare…
srs1085
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Plotting tree in R with node labels

I am trying to plot a tree with previously specified node labels in Newick…
Alex galvez morante
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Compute and plot bootstrap values with ggtree

I have a file with the phylogenetic tree that is the output of doing RAxML. I want to plot this tree with the R package ggtree and show the bootstrap values and the internal numbers of the nodes. The actual code plots the tree with the node numbers,…
Marta N
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Labels in non-leaf nodes of dendrogram in R

I want to create a graph with the classification of several items (Name1, Name2, Name3, ...) according to several criteria (Column1, Column2, Column3) in the form of a dendrogram in R (I like the orthogonal esthetics of dendrograms to this end). I…
dreamco9
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Matching node IDs of trees with the same topology

I have two phylogenetic trees which have the same topology (expect for branch lengths): In R using ape: t1 <- ape::read.tree(file="",text="(((HS:72,((CP:30,CL:30.289473923):32,RN:62):10):2,(CS:63,BS:63):11):5,LA:79);") t2 <-…
dan
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Obtaining mean phylogenetic tree branch lengths from an ensemble of phylogenetic trees

I have a set of phylogenetic trees, some with different topologies and different branch lengths. Here and example…
dan
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Looking for a better choice for real time push notification with PHP

I want to implement real time push notifications from php to my project. i already testet 2 possible ways. long polling the mysql database -> very poor performance, cause the query is big long polling memcache and push via php -> poor…
Philipp Spiess
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How can I create circular cladograms in R?

I want to produce a circular cladogram in R. I was trying out the ape package and could produce something like this: plot(tree,'f', use.edge.length=F) Now I am not really happy with how the edges look like here. I tried out the evolview webserver,…
Alex
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Add a title to a DNA bin plot in R

The R package ape allows us to create a plot of a DNAbin class object which contains information on DNA sequence alignments. Suppose I have a DNAbin object called myDNAbin. I can use > image.DNAbin(myDNAbin) to generate a plot of the sequence…
NM_
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Phylogeny Comparison to have Nodes & Tip Labels Coloured according to Tip Labels

I have plotted two phylogenetic trees face-to-face using cophylo function in phytools, and would like to colour the nodes and tip labels according to their label. plot(cophylo(T1RnB,T2RnB,assoc=assoc)) Example of tip…
web
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How to detect a page refresh using javascript on APEX?

My goal is to do some javascript action the moment the user clicks the browser's refresh button. I've tried: Function and Global Variable Declaration function pageunload(){ alert('here'); }; Execute when Page…
ItzBunzy
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Accessing a remote APE server

I am a newbie in APE. I have a linux machine that runs the APE server. I would like my .NET program running in another windows machine to connect to the APE server. How do i do it ? Both the machines are on LAN. I tried to do it by And i modified…
CuriousCoder
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Getting different test results between Moran.I and moran.test

I tried to run Moran's I test for the spatial autocorrelation test by using the function Moran.Ifrom the package ape and moran.test from the package spdep I got different results by applying the two methods on the same data. So at this point why…
user1988
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Creating a vector using tree$edge rows

I would like to create a vector of names using the tree$edge rows of a phylogenetic tree. How can I construct this vector? Example: tree$edge # object [,1] [,2] [1,] 82 83 [2,] 83 84 [3,] 84 85 [4,] 85 86 [5,] 86 …
BMT
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