phylotools: Phylogenetic tools for Eco-phylogenetics

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.

Author
Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Date of publication
2012-10-29 08:59:27
Maintainer
Jinlong Zhang <jinlongzhang01@gmail.com>
License
GPL-2
Version
0.1.2

View on CRAN

Man pages

add.mat
Add matrix to current matrix
aln2dat
Convert ClustalX alignment data to dataframe
appendchar
Paste character according to the longest character.
complement
Get the complement sequences
dat2phy
Convert dataframe to phylip format
del.tree.tip
Randomly Delete tree tip labels
dimension
Get the dimension of the matrix defined by "XnYm" labels
edgesub
Substitute character for a sequence from both sides.
fasta.split
Split the fasta object to fasta objects
fmatch
Find the matching index
formatXY
Formating XY label
framsub
Pattern of substitutions of a dataframe.
gini
Gini coefficient of inequality
hcreorder
Reorder the height for hclust object
imagevect
Image plot of a numeric vector
inequality
The inequality of a cutting time
meangini
Mean Gini coefficient
phy2dat
Convert phylip file to dataframe
phylocom.comdist
Calculating phylogenetic comdist using Phylocom
phylocom.comstruct
Calculating community phylogenetic structure using Phylocom
phylocom.pd
Calculate phylogenetic diversity using Phylocom
phylocom.phylosor
Calculating Phylosor similarity
phyloshuffle
Tip label shuffling of a phylogenetic tree
phylotools-package
Phylogenetic tools for ecologists
plotcut
Cutting the phylogenetic cutting pattern by a given time or...
plotscale
Rescaling the individuals occurred in a Forestry Dynamic Plot
read.phy
Read phylip file to memory.
rename.fasta
Renaming a fasta object given a reference table
resid.tree
The undeleted terminals of a phylogenetic tree
reverse
Get the reverse sequence.
rh
Generating random time between the oldest node and the latest...
rm.col
Delete specified columns for dataframe or matrix
RMPD
Ratio of mean phylogenetic distance of two phylogenetic trees
seq2fasta
Convert Seq file to fasta format
sub.tip.label
Substitute the tip labels of a phylogenetic tree
supermat
Build super matrix using PHYLIP files
uniquefasta
Deleting duplicated sequences in fasta object
write.mat
Save supermatrix

Files in this package

phylotools
phylotools/NAMESPACE
phylotools/man
phylotools/man/phylocom.comdist.Rd
phylotools/man/dat2phy.Rd
phylotools/man/rename.fasta.Rd
phylotools/man/rh.Rd
phylotools/man/edgesub.Rd
phylotools/man/RMPD.Rd
phylotools/man/seq2fasta.Rd
phylotools/man/gini.Rd
phylotools/man/supermat.Rd
phylotools/man/framsub.Rd
phylotools/man/dimension.Rd
phylotools/man/hcreorder.Rd
phylotools/man/uniquefasta.Rd
phylotools/man/rm.col.Rd
phylotools/man/appendchar.Rd
phylotools/man/write.mat.Rd
phylotools/man/resid.tree.Rd
phylotools/man/read.phy.Rd
phylotools/man/phylocom.pd.Rd
phylotools/man/reverse.Rd
phylotools/man/formatXY.Rd
phylotools/man/complement.Rd
phylotools/man/meangini.Rd
phylotools/man/inequality.Rd
phylotools/man/fmatch.Rd
phylotools/man/plotcut.Rd
phylotools/man/fasta.split.Rd
phylotools/man/add.mat.Rd
phylotools/man/phylocom.phylosor.Rd
phylotools/man/plotscale.Rd
phylotools/man/phy2dat.Rd
phylotools/man/sub.tip.label.Rd
phylotools/man/imagevect.Rd
phylotools/man/phylotools-package.Rd
phylotools/man/phylocom.comstruct.Rd
phylotools/man/del.tree.tip.Rd
phylotools/man/aln2dat.Rd
phylotools/man/phyloshuffle.Rd
phylotools/inst
phylotools/inst/extdata
phylotools/inst/extdata/trn2.phy
phylotools/inst/extdata/trn4.phy
phylotools/inst/extdata/aln
phylotools/inst/extdata/trn3.phy
phylotools/inst/extdata/trn1.phy
phylotools/inst/extdata/rbcla.phy
phylotools/inst/extdata/DNAman.seq
phylotools/inst/extdata/matK.phy
phylotools/inst/extdata/MC1-MF.ab1
phylotools/DESCRIPTION
phylotools/MD5
phylotools/R
phylotools/R/rename.fasta.R
phylotools/R/read.phylip.R
phylotools/R/phy2dat.R
phylotools/R/reverse.R
phylotools/R/phylocom.phylosor.R
phylotools/R/phyloshuffle.R
phylotools/R/supermat.R
phylotools/R/inequality.R
phylotools/R/dimension.R
phylotools/R/write.mat.R
phylotools/R/plotscale.R
phylotools/R/gini.R
phylotools/R/aln2dat.R
phylotools/R/hcreorder.R
phylotools/R/uniquefasta.R
phylotools/R/phylocom.comstruct.R
phylotools/R/sub.tip.label.R
phylotools/R/complement.r
phylotools/R/dat2phy.R
phylotools/R/framsub.R
phylotools/R/resid.tree.R
phylotools/R/fasta.split.R
phylotools/R/add.mat.R
phylotools/R/seq2fasta.r
phylotools/R/appendchar.R
phylotools/R/fmatch.R
phylotools/R/rm.col.R
phylotools/R/formatXY.R
phylotools/R/meangini.R
phylotools/R/plotcut.R
phylotools/R/phylocom.pd.R
phylotools/R/phylocom.comdist.R
phylotools/R/rh.R
phylotools/R/imagevect.R
phylotools/R/del.tree.tip.R
phylotools/R/edgesub.R
phylotools/R/RMPD.R