Displaying 7 results from an estimated 7 matches for "phylograms".
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phylogram
2017 Jun 19
0
New package: phylogram
Dear all,
I'd like to introduce a new R package called *phylogram,* for working with
evolutionary trees as deeply-nested lists known as "dendrogram" objects.
The package provides functions for importing and exporting phylogenetic
trees in the Newick parenthetic text format, as well as several functions
for command-line tree manipulation.
With an emphasis on speed and computational
2007 Jul 27
0
heatmap and phylogram / dendogram ploting problem
...rongly ordered and don't correspond to the Rowv dendrogram. I know
there is a bug with the heatmap fonction. Emmanuel Paradis
(http://tolstoy.newcastle.edu.au/R/e2/help/07/05/16227.html )suggested a
modification to fix it but in my case the row labels are still wrongly
ordered.
Heatmaps with 2 phylograms have been published in different papers, so a
solution exists to fix this bug. Could anyone help me ?
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2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
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
2006 Oct 17
1
ape -- internal nodes and pie charts
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.
2017 Aug 31
0
The aphid package for analysis with profile hidden Markov models
Hi folks,
I'm pleased to introduce a new package called ?aphid?, for analysis with
profile hidden Markov models in R.
The package contains functions for multiple and pairwise sequence alignment
for both nucleic acids and proteins (preferably in the DNAbin or AAbin
format), model building, parameter optimization (Baum Welch and Viterbi
training), plotting, file import & export,
2013 Jan 18
1
Hclust tree to Figtree w/ branch lengths
Hi,
I'm doing hierarchical clustering, and want to export my dendrogram to a
tree-viewing/editing software. I can do this by converting the data to
Newick format (hc2Newick in ctc package), but I can't get branch lengths to
show in the resulting phylogram. I figured it might help to convert my
hclust object into a phylo object (as.phylo in ape package), but the
following lines give me
2017 Aug 31
0
The aphid package for analysis with profile hidden Markov models
Hi folks,
I'm pleased to introduce a new package called ?aphid?, for analysis with
profile hidden Markov models in R.
The package contains functions for multiple and pairwise sequence alignment
for both nucleic acids and proteins (preferably in the DNAbin or AAbin
format), model building, parameter optimization (Baum Welch and Viterbi
training), plotting, file import & export,