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phylotools (version 0.1.2)

Phylogenetic tools for Eco-phylogenetics

Description

Building supermatrix for DNA barcodes using different genes, calculating the inequality among lineages and phylogenetic similarity for very large dataset using slicing methods by invoking Phylocom.

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Version

Install

install.packages('phylotools')

Monthly Downloads

521

Version

0.1.2

License

GPL-2

Maintainer

Jinlong Zhang

Last Published

October 29th, 2012

Functions in phylotools (0.1.2)

edgesub

Substitute character for a sequence from both sides.
appendchar

Paste character according to the longest character.
formatXY

Formating XY label
fmatch

Find the matching index
dimension

Get the dimension of the matrix defined by "XnYm" labels
dat2phy

Convert dataframe to phylip format
complement

Get the complement sequences
RMPD

Ratio of mean phylogenetic distance of two phylogenetic trees
phyloshuffle

Tip label shuffling of a phylogenetic tree
meangini

Mean Gini coefficient
rh

Generating random time between the oldest node and the latest node
gini

Gini coefficient of inequality
phylocom.pd

Calculate phylogenetic diversity using Phylocom
hcreorder

Reorder the height for hclust object
rm.col

Delete specified columns for dataframe or matrix
supermat

Build super matrix using PHYLIP files
phylocom.phylosor

Calculating Phylosor similarity
seq2fasta

Convert Seq file to fasta format
rename.fasta

Renaming a fasta object given a reference table
aln2dat

Convert ClustalX alignment data to dataframe
uniquefasta

Deleting duplicated sequences in fasta object
inequality

The inequality of a cutting time
plotscale

Rescaling the individuals occurred in a Forestry Dynamic Plot
plotcut

Cutting the phylogenetic cutting pattern by a given time or times
fasta.split

Split the fasta object to fasta objects
reverse

Get the reverse sequence.
del.tree.tip

Randomly Delete tree tip labels
resid.tree

The undeleted terminals of a phylogenetic tree
phy2dat

Convert phylip file to dataframe
add.mat

Add matrix to current matrix
read.phylip

Read phylip file to memory.
phylotools-package

Phylogenetic tools for ecologists
framsub

Pattern of substitutions of a dataframe.
imagevect

Image plot of a numeric vector
phylocom.comdist

Calculating phylogenetic comdist using Phylocom
phylocom.comstruct

Calculating community phylogenetic structure using Phylocom
write.mat

Save supermatrix
sub.tip.label

Substitute the tip labels of a phylogenetic tree