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.

AuthorJinlong Zhang, Nancai Pei, Xiangcheng Mi
Date of publication2012-10-29 08:59:27
MaintainerJinlong Zhang <jinlongzhang01@gmail.com>
LicenseGPL-2
Version0.1.2

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.