In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

knitr::opts_chunk$set(echo = TRUE, collapse=TRUE, fig.path = "README_figs/README-")

require(rePhylo)

barc<-readRDS("data/barplotMulticf.rds")
print(barc$groupings)

Overview

This package is desinged for improving phylogenies and related analyses based on phylogenies. One of the main function is to select potential paralogs by given groupings / constraints, either for another turn of phylogenetic reconstructions for an improved phylogeny, or for in-depth analysis for the phylogenetic inconsistencies.

Description and notes

cladeFilter reports, for each gene tree of trees, tips as potential paralogs that separate from others in the same groupings provided in taxa. Users can provide taxa directly, or generate one by concor.node and createGrouping. IMPORTANT NOTE: The grouping/constraints must be chosen with caution. Avoid any aribitrary selections of particular relatioships; use well-confirmed relationship unless for special purpose.

Installation

#install.packages("rePhylo")

Usage and examples

First get the datasets:

data("Brassidata")
trees <- Brassidata$trees
taxa <- Brassidata$taxaTable
ref <- Brassidata$ref

trees contains all gene trees to be investigated as a list.

taxa is a data.frame that gives grouping information. The first column must be tip names in any of the test trees (gene trees).

ref is a reference tree (when using Method 1)

Method 1

#concorn <- concor.node(ref = ref, trees = trees, bp = c(0, 30, 50), getTreeNames = FALSE)
#groups <- createGrouping(concor = concorn, percent = 0.7)
#head(groups)