BoSSA-package {BoSSA} | R Documentation |
A Bunch of Structure and Sequence Analysis
Description
Reads and plots phylogenetic placements.
Details
The DESCRIPTION file:
Package: | BoSSA |
Type: | Package |
Title: | A Bunch of Structure and Sequence Analysis |
Version: | 3.7 |
Date: | 2020-10-16 |
Author: | Pierre Lefeuvre |
Maintainer: | Pierre Lefeuvre <pierre.lefeuvre@cirad.fr> |
Depends: | R (>= 3.3.0) |
Imports: | ape, RSQLite, jsonlite, phangorn, plotrix |
Suggests: | prettydoc, knitr, rmarkdown, XML, rentrez, httr |
VignetteBuilder: | knitr |
Description: | Reads and plots phylogenetic placements. |
License: | GPL |
Index of help topics:
BoSSA-package A Bunch of Structure and Sequence Analysis circular_tree Plot an inside-out circular tree plot.pplace Plot a pplace or jplace object pplace A placement object as obtained with the read_sqlite function pplace_to_matrix Pplace to contingency matrix pplace_to_table Merge the multiclass and the placement table of pplace object pplace_to_taxonomy Convert a pplace object to a taxonomy table print.pplace Compact display of pplace and jplace objects print.protdb Compact display of protdb object read_jplace Read a jplace file read_protdb Read Protein Data Bank (PDB) file read_sqlite Read a pplacer/guppy sqlite file refpkg Summary data and plots for reference packages sub_pplace Subsets a pplace object write_jplace Write a jplace or pplace object to the disk
BoSSA contains functions to read and plot phylogenetic placement files obtained using softwares such as pplacer, guppy, EPA and RAPPAS.
Author(s)
Pierre Lefeuvre Maintainer: Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>
References
- pplacer and guppy http://matsen.fhcrc.org/pplacer/ http://matsen.github.io/pplacer/ - EPA https://sco.h-its.org/exelixis/web/software/epa/index.html - RAPPAS https://github.com/benclaff/RAPPAS - Common file format http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009
[Package BoSSA version 3.7 Index]