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phylotools (version 0.1.1)

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

393

Version

0.1.1

License

GPL-2

Maintainer

Jinlong Zhang

Last Published

July 23rd, 2011

Functions in phylotools (0.1.1)

edgesub

Substitute character for a sequence from both sides.
dat2phy

Convert dataframe to phylip format
fasta.split

Split the fasta object to fasta objects
RMPD

Ratio of mean phylogenetic distance of two phylogenetic trees
appendchar

Paste character according to the longest character.
complement

Get the complement sequences
dimension

Get the dimension of the matrix defined by "XnYm" labels
read.phylip

Read phylip file to memory.
aln2dat

Convert ClustalX alignment data to dataframe
rh

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

Reorder the height for hclust object
phylocom.comdist

Calculating phylogenetic comdist using Phylocom
rm.col

Delete specified columns for dataframe or matrix
plotscale

Rescaling the individuals occurred in a Forestry Dynamic Plot
add.mat

Add matrix to current matrix
seq2fasta

Convert Seq file to fasta format
formatXY

Formating XY label
phylocom.phylosor

Calculating Phylosor similarity
rename.fasta

Renaming a fasta object given a reference table
inequality

The inequality of a cutting time
reverse

Get the reverse sequence.
uniquefasta

Deleting duplicated sequences in fasta object
fmatch

Find the matching index
plotcut

Cutting the phylogenetic cutting pattern by a given time or times
phy2dat

Convert phylip file to dataframe
imagevect

Image plot of a numeric vector
phylocom.pd

Calculate phylogenetic diversity using Phylocom
sub.tip.label

Substitute the tip labels of a phylogenetic tree
write.mat

Save supermatrix
supermat

Build super matrix using PHYLIP files
phylotools-package

Phylogenetic tools for ecologists
phylocom.comstruct

Calculating community phylogenetic structure using Phylocom
resid.tree

The undeleted terminals of a phylogenetic tree
phyloshuffle

Tip label shuffling of a phylogenetic tree
gini

Gini coefficient of inequality
del.tree.tip

Randomly Delete tree tip labels
framsub

Pattern of substitutions of a dataframe.
meangini

Mean Gini coefficient