README.md

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

rePhylo: Re-investigating and improving phylogenies

Overview

This package is to improve phylogenies based on phylogenies. One of the main function is to select potential paralogs by given groupings / constraints, and the users can perform another turn of phylogenetic reconstructions for an improved phylogeny.

Description and notes

cladeFilter reports tips as potential paralogs that violate the groupings provided in taxa for each gene tree of trees. Users can provide taxa directly, or generate one by concor.node and createGrouping. IMPORTANT NOTE: The grouping/constraints must be chosen very carefully. Avoid any aribitrary selections of particular relatioships; suggested to use the 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)

Method 2

head(taxa)
##                                     tips clades
## 1            Rorippa_globosa_Cardamineae cladeA
## 2         Rorippa_sylvestris_Cardamineae cladeA
## 3             Rorippa_indica_Cardamineae cladeA
## 4 Leavenworthia_alabamica_ge_Cardamineae cladeA
## 5          Barbarea_vulgaris_Cardamineae cladeA
## 6       Cardamine_hirsute_ge_Cardamineae cladeA

Details

...under construction

Chien-Hsun/rePhylo documentation built on May 19, 2020, 3:15 a.m.