BoSSA-package {BoSSA}

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 <[e-mail]>
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 <[e-mail]>

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