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 efficiency, the *phylogram* package
also includes tools for rapidly computing distance matrices, and building
large trees using fast alignment-free k-mer counting and divisive
clustering. While not guaranteed to produce sufficiently accurate
phylogenetic trees for taxonomic purposes, this offers an efficient means
of clustering large trees for a variety of other applications including
tree-based sequence weighting, guide trees for progressive multiple
sequence alignment, and other recursive operations such as classification
tree learning.
Any feedback is warmly welcomed.
vignette:
https://cran.r-project.org/web/packages/phylogram/vignettes/phylogram-vignette.html
development version: https://github.com/shaunpwilkinson/phylogram
bug reports: https://github.com/shaunpwilkinson/phylogram/issues
google group: https://groups.google.com/group/phylogram
Best regards,
Shaun Wilkinson
Email: shaunpwilkinson at gmail.com
Twitter: @wilkinshau
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