Interfaces to Phylogenetic Software

Description

This package presents a set of functions that were formerly included in the phyloch package and which wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

Details

There are several functions for reading and writing DNA sequences in FASTA, PHYLIP, and NEXUS format: read.fas, read.phy, read.nex, write.fas, write.phy, and write.nex. Some functions are available for integrating BEAST with R. XML input files for BEAST can be generated with rbeauti. Two functions are designed to read TreeAnnotator output: read.beast will render an object of class phylo with additional node statistics appended as list elements. These additional node statistics will be lost be the subsequent use of ladderize or rotate (or similar functions that change the ordering of internal nodes).read.beast.table also parses the TreeAnnotator output, but returns a matrix of node statistics. This package itself does not implement techniques for phylogenetic analyses, but provides a series of wrappers for commonly used software packages. Sequence alignment can be done with the mafft and prank; cleaning of sequences with gblocks and aliscore. The function raxml and mrbayes are intended for phylogenetic tree search. Running mrbayes with argument run = FALSE can be used to create MrBayes-executable NEXUS files. Finally, wrappers is provided for Multistate in the BayesTraits package (see multistateML and multistateMCMC). Several plotting functions (HPDbars, clade.bars, box.clades, box.tips, tip.color, edge.color have been moved to the viper package.

Author(s)

Natalie Cusimano, Christoph Heibl, Franz-Sebastian Krah, Maintainer: Christoph Heibl (christoph.heibl@gmx.net)

See Also

ape

Conversion of DNAbin to Index

Description

Extract the indices of non-empty positions in a sample of DNA sequences to

Usage

DNAbin2index(x)

Arguments

See Also

index2DNAbin

Identify/Delete Spurious Rows and Columns from DNA Alignments

Description

After subsetting (see e.g. DNAbin), DNA sequence alignments can contain rows and columns that consist entirely of missing and/or ambiguous character states. identifyEmptyCells will identify and deleteEmptyCells will delete all such rows (taxa) and columns (characters) from a DNA sequence alignment.

Usage

deleteEmptyCells(
  DNAbin,
  margin = c(1, 2),
  nset = c("-", "n", "?"),
  quiet = FALSE
)

identifyEmptyCells(
  DNAbin,
  margin = c(1, 2),
  nset = c("-", "n", "?"),
  quiet = FALSE
)

Arguments

Details

For faster execution, deleteEmptyCells handles sequences in ape's bit-level coding scheme.

Value

An object of class DNAbin.

References

Cornish-Bowden, A. 1984. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 13: 3021–3030.

See Also

trimEnds, deleteGaps

Examples

  # COX1 sequences of bark beetles
  data(ips.cox1)
  # introduce completely ambiguous rows and colums
  x <- as.character(ips.cox1[1:6, 1:60])
  x[3, ] <- rep("n", 60)
  x[, 20:24] <- rep("-", 6)
  x <- as.DNAbin(x)
  image(x)
  # identify those rows and colums
  (id <- identifyEmptyCells(x))
  xx <- x[-id$row, -id$col]
  # delete those rows and colums
  x <- deleteEmptyCells(x)
  image(x)
  identical(x, xx)

Masking of Sequence Alignments with ALISCORE

Description

Provides a interface to Aliscore, in order to remove problematic regions of a DNA sequence alignment.

Usage

aliscore(x, gaps = "5state", w = 6, r, t, l, s, o, exec)

Arguments

Value

A matrix of class "DNAbin".

Note

This function was developed with ALISCORE version 2.

References

Misof, B. and K. Misof. 2009. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst. Biol. 58: 21–34.

Kueck, P., K. Meusemann, J. Dambach, B. Thormann, B.M. von Reumont, J.W. Waegele and B. Misof. 2010. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Frontiers in Zoology 7: 10.

Aliscore website: https://bonn.leibniz-lib.de/en/research/research-centres-and-groups/aliscore

See Also

mafft and prank for multiple sequence alignment; gblocks for another alignment masking algorithm.

Examples

data(ips.28S)
## Not run: aliscore(ips.28S)

XML Parameter Nodes

Description

A collection of parameter nodes used in the standard template of BEAST2.

Usage

beastLog(l, x, i)

Arguments

Value

An object of class XMLNode.

Nucleotide-Nucleotide BLAST

Description

Provides an interface to BLASTN

Usage

blastn(query, db)

Arguments

Simple Gap/Indel Coding

Description

code.simple.gaps takes an aligned DNA sequence matrix and codes the simple gaps, i.e. gaps that do not overlap with other gaps. The gapped positions are excluded from the matrix and the coded gap characters are appended to the matrix.

Usage

code.simple.gaps(x, append = TRUE)

Arguments

Value

An object of class DNAbin.

Author(s)

Christoph Heibl

References

Simmons, M.P. & H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49(2): 369–381.

See Also

deleteGaps, deleteEmptyCells, trimEnds

Collapse Unsupported Edges/Branches in a Phylogeny

Description

Given a set of node support values (e.g., bootstrap proportions, posterior probabilities) and a certain threshold, all edges receiving less support than the threshold will be collapsed.

Usage

collapseUnsupportedEdges(phy, value = "node.label", cutoff)

Arguments

Value

An object of class phylo.

Examples

## phylogeny of bark beetles
data(ips.tree)
## non-parametric bootstrap proportions (BP)
ips.tree$node.label
## collapse clades with < 70 BP
tr <- collapseUnsupportedEdges(ips.tree, "node.label", 70)
## show new topology
par(mfrow = c(1, 2))
plot(ips.tree, no.margin = TRUE)
nodelabels(ips.tree$node.label, cex = .5, frame = "n", adj = c(0, .5))
plot(tr, no.margin = TRUE)

Graft Polytomies on Tips of Phylogeny

Description

Graft polytomies on the tips of a class phylo object.

Usage

combMyTree(phy, data, brlen = 0, annotate = FALSE)

Arguments

Value

An object of class phylo with nrow(data) tips.

See Also

forceEqualTipHeights

Examples

data(ips.tree)
## Simulate varying number of intraspecific observations
s <- sapply(1:Ntip(ips.tree), sample, x = 1:3, size = 1)
x <- rep(ips.tree$tip.label, times = s)
x <- data.frame(x, paste0(x, unlist(lapply(s, function(z) 1:z))))
## Create polytomies
tre <- combMyTree(ips.tree, x)
plot(tre, no.margin = TRUE, cex =.5)

Delete Missing Data from DNA Sequences

Description

Remove gaps ("-") and/or missing and ambiguous data ("N", "?") from a sample of DNA sequences.

Usage

del.miss(x)

Arguments

Value

A list or a vector of class DNAbin.

Remove Gap Positions From DNA Sequences

Description

Remove indel positions (or gaps) from a DNA sequence alignment. For faster execution, deleteGaps handles sequences in ape's bit-level coding scheme.

Usage

deleteGaps(x, gap.max = nrow(x) - 4)

Arguments

Details

The default, nmax = nrow(x) - 4, removes all those positions from the alignment, which contain at least four non-gap characters, which is the minimum number of sequences needed to produce a non-trivial unrooted topology. All gaps will be excluded by selecting nmax = 0 and half of all gaps with nmax = nrow(x) / 2.

In contrast, del.gaps removes all gap characters from the alignment, so most probably the result will not be a set of sequences of equal length and the matrix will be coerced to a list.

Value

An object of class DNAbin.

See Also

code.simple.gaps for coding of simple gaps, del.gaps for removal of all gap symbols from an alignment, gblocks and aliscore for more sophisticated methods of cleaning/masking alignments.

Descendants of an Internal Node in a Phylogeny

Description

For any given internal node of a phylogeny, the function returns a vector containing the node numbers descending from that node.

Usage

descendants(phy, node, type = "t", ignore.tip = TRUE, labels = FALSE)

Arguments

Value

A vector containing terminal node numbers or tip labels.

Author(s)

Christoph Heibl

See Also

sister, noi

Examples

 # generate a random tree with 12 terminal and 11 internal nodes:
 tree <- rtree(12)
 
 # get the descendants of internal node 15:
 x <- descendants(tree, 15)

Identification of Stem-Lineage-Edges and MRCAs

Description

noi (node of interest) identifies the most recent common ancestor (MRCA) and eoi (edge of interest) its subtending stem-lineage edge of one or more sets of taxa/tips.

Usage

eoi(phy, node, group, regex = FALSE, stem = FALSE, monophyletic = FALSE)

noi(phy, group, regex = FALSE, stem = FALSE, monophyletic = FALSE)

Arguments

Value

A vector of mode "numeric" containing node numbers.

See Also

mrca; descendants for the contrary operation to noi.

Examples

# molecular phylogeny of Ips bark beetles
# ---------------------------------------
data(ips.tree)
ips.tree <- ladderize(ips.tree)
ips.tree <- fixNodes(ips.tree)
clade1 <- descendants(ips.tree, 44, labels = TRUE)
mrca <- noi(ips.tree, clade1)
stem_lineage <- eoi(ips.tree, mrca)
ecol <- rep("black", Nedge(ips.tree))
ecol[stem_lineage] <- "red"
plot(ips.tree, no.margin = TRUE, edge.color = ecol)
nodelabels(node = mrca, pch = 22, col = "blue")
#gen <- sapply(viperidae$tip.label, function(x) unlist(strsplit(x, "_"))[1])
#tax <- data.frame(genus = gen, species = viperidae$tip.label, row.names = NULL)

# group can be a list
# -------------------
#myclades <- split(tax$species, tax$genus)
#nds <- noi(viperidae, myclades)
#plot(viperidae)
#nodeInfo(nds)

# group might contain tip numbers
# -------------------------------
#group <- list(c(17, 22), c(13, 1))
#plot(viperidae)
#append2tips(phy, tips = unlist(group), pch = 19)
#nds <- noi(viperidae, myclades)
#nodeInfo(nds)

# the 'group' argument can also take regular expressions
# ------------------------------------------------------
#rex <- "aspis"
#node <- noi(viperidae, rex, regex = TRUE)
#plot.phylo(viperidae, tip.color = 0, edge.color = 0)
#box.clades(viperidae, nodes = node, col = "#D2A6A7", align = "all")
#plot.phylo.upon(viperidae)
#nodelabels(node = node, pch = 21, cex = 1.2, col = "red", bg = "#D2A6A7")

# if the 'group' argument is a list of elements of length 2,
# n = length(group) nodes of interest will be returned
# ----------------------------------------------------
#group <- list(
#    c("Vipera_berus", "Vipera_ursinii"),
#    c("Vipera_aspis_ssp._aspis", "Vipera_latastei"),
#    c("Vipera_ammodytes_ssp._ammodytes",
#        "Vipera_ammodytes_ssp._montandoni"),
#    c("Macrovipera_lebetina", "Vipera_wagneri")
#)
#clades <- noi(viperidae, group)
#plot.phylo(viperidae, tip.color = 0, edge.color = 0)
#box.clades(viperidae, nodes = clades, col = c("#FFFFA5", "#D2A6A7",
#    "#A7D2A5", "#A5A6D2"), align = "all")
#plot.phylo.upon(viperidae)

Standard Node Numbering in Phylo Objects

Description

The function (re-)establishes the standard numbering of terminal and internal nodes in phylogenies represented as objects of class phylo.

Usage

fixNodes(phy)

Arguments

Details

When reading phylogenetic trees from a NEXUS file that contains a translate section, it can happen that the terminal nodes (tips, leaves) of the corresponding phylo object are not numbered consecutively, which can be a problem in some downstream applications. You can use fixNodes to get the correct order of terminal node numbers.

fixNodes is also intended to re-establish the standard numbering of internal nodes and reorder all node value elements (e.g. node.label, posterior, ...) if a phylo object has been modified by either root, ladderize, or rotate.

Value

An object of class phylo.

Note

fixNodes has been completely rewritten for ips version 1.0-0. It should now run absolutely stable and is much quicker. Nevertheless, I recommend checking carefully the results of fixNodes, until the function has been tested by a number of users. Then this comment will be removed.

Author(s)

Christoph Heibl

See Also

read.tree, read.nexus, read.beast for reading trees in NEWICK and NEXUS format; ladderize and rotate for tree manipulation; node.support for plotting node support values has been moved to package viper.

Equal Tip Heights

Description

Modify terminal edge lengths to create "exactly" (see Details) equal tip heights (sum of edge lengths from root to tip)

Usage

forceEqualTipHeights(phy, baseline = "mean")

Arguments

Details

What is "exactly" equal depends on the precision of the system (.Machine); in any case the resulting phylogeny will pass is.ultrametric with default arguments.

Value

An object of class phylo with changed terminal edge lengths.

Note

forceEqualTipHeights is only intended to correct small rounding errors in edge lengths, not to make an additive phylogeny ultrametric. For the latter, see e.g. chronos.

See Also

tipHeights

Masking of Sequence Alignments with GBLOCKS

Description

Provides a wrapper to Gblocks, a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. Gblocks selects conserved blocks from a multiple alignment according to a set of features of the alignment positions.

Usage

gblocks(
  x,
  b1 = 0.5,
  b2 = b1,
  b3 = ncol(x),
  b4 = 2,
  b5 = "a",
  target = "alignment",
  exec
)

Arguments

Details

Explanation of the routine taken from the Online Documentation: First, the degree of conservation of every positions of the multiple alignment is evaluated and classified as nonconserved, conserved, or highly conserved. All stretches of contiguous nonconserved positions bigger than a certain value (b3) are rejected. In such stretches, alignments are normally ambiguous and, even when in some cases a unique alignment could be given, multiple hidden substitutions make them inadequate for phylogenetic analysis. In the remaining blocks, flanks are examined and positions are removed until blocks are surrounded by highly conserved positions at both flanks. This way, selected blocks are anchored by positions that can be aligned with high confidence. Then, all gap positions -that can be defined in three different ways (b5)- are removed. Furthermore, nonconserved positions adjacent to a gap position are also eliminated until a conserved position is reached, because regions adjacent to a gap are the most difficult to align. Finally, small blocks (falling below the limit of b4) remaining after gap cleaning are also removed.

Value

A matrix of class "DNAbin"

Note

gblocks was last updated and tested to work with Gblocks 0.91b. If you have problems getting the function to work with a newer version of Gblocks, please contact the package maintainer.

References

Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552.

Talavera, G., and J. Castresana. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56, 564-577.

Gblocks website: https://www.biologiaevolutiva.org/jcastresana/Gblocks.html

See Also

mafft and prank for multiple sequence alignment; aliscore for another alignment masking algorithm.

Examples

data(ips.28S)
## Not run: gblocks(ips.28S)  

Conversion of Index to DNAbin

Description

Use indices of non-empty positions to convert a list of DNA sequences into a matrix.

Usage

index2DNAbin(DNAbin, index)

Arguments

See Also

DNAbin2index

Internal IPS Functions

Description

Internal ips functions.

Note

These are internal functions in ips and are not intended to be called by the user.

Bark Beetle 16S Sequences

Description

This DNA alignment contains 376 positions of 42 sequences of 16S ribosomal DNA of the bark beetle genera Ips, Orthotomicus, and Pityogenes (Scolytinae, Curculionidae, Coleoptera).

Usage

data(ips.16S)

Format

The sequences are stored in binary format (see DNAbin).

Source

The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014.

References

The nucleotide database on the NCBI website: https://www.ncbi.nlm.nih.gov/nuccore

Examples

data(ips.16S)

Bark Beetle 28S Sequences

Description

This DNA alignment contains 562 positions of 28 sequences of 28S ribosomal DNA of the bark beetle genus Ips (Scolytinae, Curculionidae, Coleoptera).

Usage

data(ips.28S)

Format

The sequences are stored in binary format (see DNAbin).

Source

The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014.

References

The nucleotide database on the NCBI website: https://www.ncbi.nlm.nih.gov/nuccore

Examples

data(ips.28S)

Bark Beetle COX1 Sequences

Description

This DNA alignment contains 770 positions of 26 sequences of cox1 of the bark beetle genera Ips, Orthotomicus, and Pityogenes (Scolytinae, Curculionidae, Coleoptera).

Usage

data(ips.cox1)

Format

The sequences are stored in binary format (see DNAbin).

Source

The sequences were downloaded and assembled from the Nucleotide repository at GenBank on February 8, 2014.

References

The nucleotide database on the NCBI website: https://www.ncbi.nlm.nih.gov/nuccore

Examples

data(ips.cox1)

Ips Phylogeny

Description

Phylogenetic tree of bark beetles (genus Ips).

Usage

data(ips.tree)

Format

The format is: List of 5 $ edge : int [1:72, 1:2] 38 39 39 40 41 42 42 43 44 45 ... $ Nnode : int 36 $ tip.label : chr [1:37] "Ips_acuminatus" "Ips_duplicatus" "Ips_integer" "Ips_plastographus" ... $ edge.length: num [1:72] 0.2806 0.0727 0.0295 0.0097 0.021 ... $ node.label : chr [1:36] "" "100" "21" "12" ... - attr(*, "class")= chr "phylo" - attr(*, "order")= chr "cladewise"

Examples

data(ips.tree)
plot(ips.tree)

Sequence Alignment with MAFFT

Description

This function is a wrapper for MAFFT and can be used for (profile) aligning of DNA and amino acid sequences.

Usage

mafft(
  x,
  y,
  add,
  method = "auto",
  maxiterate = 0,
  op = 1.53,
  ep = 0,
  gt = NULL,
  options,
  thread = -1,
  exec,
  quiet,
  file
)

Arguments

Details

"localpair" selects the L-INS-i algorithm, probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information.

"globalpair" selects the G-INS-i algorithm suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information.

"genafpair" selects the E-INS-i algorithm suitable for sequences containing large unalignable regions; recommended for <200 sequences.

"retree 1" selects the FFT-NS-1 algorithm, the simplest progressive option in MAFFT; recommended for >200 sequences.

"retree 2" selects the FFT-NS-2 algorithm that uses a second iteration of alignment based on a guide tree computed from an FFT-NS-1 alignment; this is the default in MAFFT; recommended for >200 sequences.

Value

A matrix of class "DNAbin" or "AAbin".

Note

mafft was last updated and tested to work with MAFFT 7.205. If you have problems getting the function to work with a newer version of MAFFT, please contact the package maintainer.

References

Katoh, K. and H. Toh. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298.

Katoh, K., K.-i. Kuma, H. Toh, and T. Miyata. 2005. Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511–518.

Katoh, K., K. Misawa, K.-i. Kuma, and T. Miyata. 2002. Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleid Acids Research 30: 3059–3066.

https://mafft.cbrc.jp/alignment/software/index.html

See Also

read.fas to import DNA sequences; prank for another alignment algorithm; gblocks and aliscore for alignment cleaning.

Profile Alignment with MAFFT

Description

Merge two or more DNA or amino acid sequence alignments by profile alignment with MAFFT.

Usage

mafft.merge(subMSA, method = "auto", gt, thread = -1, exec, quiet = TRUE)

Arguments

Value

An object of class "DNAbin" or "AAbin".

Bayesian MCMC Tree Search with MrBayes

Description

Provides a wrapper for Bayesian phylogenetic tree search through MrBayes (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003).

Usage

mrbayes(
  x,
  file = "",
  lset,
  prset,
  mcmc,
  unlink,
  constraint,
  burnin = 10,
  contype = "allcompat",
  exec,
  run = FALSE
)

Arguments

Details

mrbayes was last updated and tested with MrBayes v3.2.2 under R 3.1.0 on a x86_64-apple-darwin10.8.0 (64-bit) platform. It is intended to offer a simply parameterized building block for larger scripts.

Value

None; a NEXUS file with MrBayes block is written to a file and, if run = TRUE, the MCMC runs in MrBayes are started.

References

J. P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755. Ronquist F. & J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574. MrBayes website: https://mrbayes.sourceforge.net/.

See Also

mafft and prank for sequence alignment; raxml for maximum likelihood tree search.

Examples

data(ips.cox1)
x <- ips.cox1[, 100:140] # tiny alignment
mrbayes(x, file = "", mcmc = mrbayes.mcmc(ngen = 100), run = FALSE)
## Not run: 
library(phangorn)
tree <- rtree(10)
Y1 <- simSeq(tree, l = 20)
Y2 <- simSeq(tree, l = 20, type = "USER", levels=c("0", "1"))
Y <- cbind(as.character(Y1), as.character(Y2))

## End(Not run)

Model Settings for MrBayes

Description

Set model parameters for mrbayes.

Usage

mrbayes.lset(..., partition)

Arguments

Value

a list containing a subset (including the empty and the full set) of model parameters.

Model Parameters

nucmodel

"4by4", "doublet", "codon", or "protein".

nst

1, 2, 6, or "mixed".

code

"universal", "vertmt", "mycoplasma", "yeast", "ciliates", or "metmt".

ploidy

"haploid", "diploid", or "zlinked".

rates

"equal", "gamma", "propinv","invgamma", or "adgamma".

ngammacat

1-24

nbetacat

1-24

omegavar

"equal", "ny98", or "m3".

covarion

"no" or "yes".

coding

"all", "variable", "noabsencesites", or "nopresencesites".

parsmodel

"no" or "yes".

Author(s)

Christoph Heibl

References

J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574.

MrBayes website: https://mrbayes.sourceforge.net/.

See Also

mrbayes.prset to set prior distributions, mrbayes.mcmc to set parameters of the Markov chain Monte Carlo (MCMC), and mrbayes to run MrBayes locally or prepare input files for a computer cluster.

Examples

## F81
mrbayes.lset(nst = 2)

## GTR + Gamma
mrbayes.lset(nst = 6, rates = "gamma")

## GTR + Gamma + I
mrbayes.lset(nst = 6, rates = "invgamma")

MCMC Settings for MrBayes

Description

Set Markov chain Monte Carlo (MCMC) parameters for mrbayes.

Usage

mrbayes.mcmc(...)

Arguments

Value

a list containing a subset (including the empty and the full set) of model parameters.

MCMC Parameters

ngen

"NUMERIC"

nruns

"NUMERIC"

nchains

"NUMERIC"

temp

"NUMERIC"

swapfreq

"NUMERIC"

nswaps

"NUMERIC"

samplefreq

"NUMERIC"

printfreq

"NUMERIC"

printall

"yes" or "no"

printmax

"NUMERIC"

mcmcdiagn

"yes" or "no"

diagnfreq

"NUMERIC"

diagnstat

"avgstddev" or "maxstddev"

minpartfreq

"NUMERIC"

allchains

"yes" or "no"

allcomps

"yes" or "no"

relburnin

"yes" or "no"

burnin

"NUMERIC"

burninfrac

"NUMERIC"

stoprule

"yes" or "no"

stopval

"NUMERIC"

savetrees

"yes" or "no"

checkpoint

"yes" or "no"

checkfreq

"NUMERIC"

startparams

"current" or "reset"

starttree

"current", "random", or "parsimony"

nperts

"NUMERIC"

data

"yes" or "no"

ordertaxa

"yes" or "no"

append

"yes" or "no"

autotune

"yes" or "no"

tunefreq

"NUMERIC"

Note

The parameters reweight and filename cannot be set via mrbayes.mcmc.

Author(s)

Christoph Heibl

References

J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574.

MrBayes website: https://mrbayes.sourceforge.net/.

See Also

mrbayes.lset to set model parameters, mrbayes.prset to set prior distributions, and mrbayes to run MrBayes locally or prepare input files for a computer cluster.

Examples

mrbayes.mcmc()

Set Priors for MrBayes

Description

Set prior distributions for mrbayes.

Usage

mrbayes.prset(...)

Arguments

Value

a list of length zero (see 'Note')

Prior Distribution Parameters

traitiopr

revmatpr

aamodelpr

aarevmatpr

omegapr

ny98omega1pr

ny98omega3pr

m3omegapr

codoncatfreqs

statefreqpr

shapepr

ratecorrpr

pinvarpr

covswitchpr

symdirihyperpr

topologypr

brlenspr

clockvarpr

igrvarpr

Note

This function currently returns an empty set of prior distribution parameters, i.e., you cannot change the MrBayes default parameters.

Author(s)

Christoph Heibl

References

J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574.

MrBayes website: https://mrbayes.sourceforge.net/.

See Also

mrbayes.lset to set model parameters, mrbayes.mcmc to set parameters of the Markov chain Monte Carlo (MCMC), and mrbayes to run MrBayes locally or prepare input files for a computer cluster.

Examples

mrbayes.prset()

MULTISTATE

Description

These functions provide wrappers to BayesMultiState in the BayesTraits package written by Mark Pagel and Andrew Meade.

Usage

multistateML(phy, traits, model = "ARD", anc.states = TRUE, 
  path = "/Applications/BayesTraits", dir = NULL)

multistateMCMC(phy, traits, model = "ARD", anc.states = TRUE, 
    rd = 2, rjhp = NULL, fixNodes = NULL, it = 1e+05, bi = 10000,
    sa = 1000, path = "/Applications/BayesTraits", dir = NULL)

Arguments

Author(s)

Christoph Heibl

References

The BayesTraits manual: http://www.evolution.reading.ac.uk/BayesTraitsV4.1.1/Files/BayesTraitsV4.1.1-Manual.pdf.

Pagel, M., A. Meade, and D. Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst. Biol. 53: 673-684.

Pagel, M. and A. Meade. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am. Nat. 167: 808-825.

See Also

ace

Neighboring Nodes in a Minimum Spanning Tree

Description

Finds all pairs of adjacent nodes, i.e. nodes separated by only one edge, in a minimum spanning tree

Usage

neighboringPairs(mst)

Arguments

Numbers of Tips of (Sub)trees

Description

Counts the number of tips of a given clade of a phylogenetic tree.

Usage

ntip(phy, node)

Arguments

Value

An integer giving the number of tips.

Examples

set.seed(1234)
tr <- rtree(12)
plot(tr); nodelabels()
ntip(tr, 16)

PartitionFinder

Description

Provides a wrapper to the PartitionFinder software.

Usage

partitionfinder(
  alignment,
  user.tree,
  branchlengths = "linked",
  models = "all",
  model.selection = "BIC",
  search = "greedy",
  exec = "/Applications/PartitionFinderV1.1.1_Mac/PartitionFinder.py"
)

Arguments

References

Lanfear, R., B. Calcott, S.Y.W. Ho, and S. Guindon. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695-1701.

Lanfear, R., B. Calcott, K. David, C. Mayer, and A. Stamatakis. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14: 82.

PATHd8

Description

This function is a wrapper for PATHd8 and can be used for phylogenetic dating, especially of large trees

Usage

pathd8(phy, exec = "/Applications/PATHd8/PATHd8", seql, calibration)

Arguments

Value

tree list of ultrametric trees returned from PATHd8 of class phylo. First tree is PATHd8 chronogram, which is a calibrated ultrametric tree. Second is a PATH tree, which is a ultrametric tree without calibration.

Author(s)

Franz-Sebastian Krah

References

Britton et al (2006). PATHd8—a new method for estimating divergence times in large phylogenetic trees without a molecular clock. Available from the authors (www.math.su.se/PATHd8)

Britton et al. (2007). Estimating divergence times in large phylogenetic trees. Systematic biology. 56:741–752

Examples

## Not run: 
## This example is taken from the PATHD8 manual
cal <- rbind(cal1 = c("Rat", "Ostrich", "minage", 260), 
cal2 = c("Human", "Platypus", "fixage", 125),
cal3 = c("Alligator", "Ostrich", "minage", 150))
colnames(cal) = c("tax1", "tax2", "age_type", "age")
phy <- read.tree(text = paste0("((((Rat:0.007148,Human:0.001808):0.024345,",
                               "Platypus:0.016588):0.012920,(Ostrich:0.018119,",
                               "Alligator:0. 006232):0.004708):0.028037,Frog:0);")
seql <- 1823
pathd8(phy, exec = "/Applications/PATHd8/PATHd8", seql = seql, calibration = cal)

## End(Not run)

Convert Trees for MAFFT

Description

Converts a phylogenetic tree of class "phylo" to a format usable as a guide tree by MAFFT. This function is called internally by mafft.

Usage

phylo2mafft(phy, file)

Arguments

Value

A matrix coding the MAFFT-formatted tree, as a side effect the same matrix is written to file.

References

The MAFFT website: https://mafft.cbrc.jp/alignment/software/index.html

See Also

mafft for an interface to MAFFT.

Conversion from PHYLO to MST Object

Description

Converts a phylogenetic tree (class phylo) into a minimum spanning tree (class mst).

Usage

phylo2mst(phy)

Arguments

Details

The current version of phylo2mst does not handle polytomies and does not incorporate branch length information. Note that topological information is lost during the conversion.

Examples

phy <- rtree(12)
plot(phy)
mst <- phylo2mst(phy)
plot(mst)

Number of Potentially-Informative Sites

Description

Returns the number or positions of potentially-informative (parsimony-informative, phylogenetically-informative) sites in DNA sequence alignment.

Usage

pis(x, what = "fraction", use.ambiguities = FALSE)

Arguments

Value

Numeric (depending on what, the number, fraction, or indices of potentially-informative nucleotide sites).

Examples

data(ips.16S)	

# number of potentially-informative sites:
pis(ips.16S, what = "abs")

# proportion of potentially-informative sites:
pis(ips.16S, what = "frac")

# indices of potentially-informative sites:
pis(ips.16S, what = "ind")

PRANK

Description

DNA sequence Alignment Using the program PRANK.

Usage

prank(x, outfile, guidetree = NULL, gaprate = 0.025, 
    gapext = 0.75, path)

Arguments

Value

matrix of class "DNAbin"

Note

prank was last updated and tested to work with PRANK v. 120814 on Windows XP. If you have problems getting the function to work with a newer version of PRANK, contact the package maintainer.

References

http://wasabiapp.org/software/prank/

See Also

read.fas to import DNA sequences; mafft for another alignment algorithm; gblocks and aliscore for alignment cleaning.

Maximum Likelihood Tree Estimation with RAxML

Description

Provides an interface to the C program RAxML (see Reference section) for maximum likelihood estimation of tree topology and/or branch lengths, rapid and conventional non-parametric bootstrapping, mapping splits onto individual topologies, and a lot more. See the RAxML manual for details, especially if you are a new user of RAxML.

Usage

raxml(
  DNAbin,
  m = "GTRCAT",
  f,
  N,
  p,
  b,
  x,
  k,
  weights,
  partitions,
  outgroup,
  backbone = NULL,
  file = paste0("fromR_", Sys.Date()),
  exec,
  threads
)

Arguments

Details

There are some limitations of this wrapper compared to RAxML run directly from the command line.

1. Only DNA is allowed as data type.

2. Option f can only take a limited number of values (d, a).

RAxML needs the specification of random seeds for parsimony estimation of starting trees and for bootstrap resampling. The corresponding argument names in raxml are identical to the flags used by RAxML (-p, -b, and -x). If you choose not to give any values, raxml will generate a (different) value for each required random seed every time it is called. Be aware that set.seed will work only for p, but not for b or x.

Value

A list with a variable number of elements, depending on the analysis chosen:

Note

RAxML is a C program and the source code is not contained in this package. This means that in order to run this function you will need to install RAxML yourself. See https://cme.h-its.org/exelixis/web/software/raxml/ for the most recent documentation and source code of RAxML. Depending on where you chose to install RAxML, you need to adjust the exec argument.

raxml was last tested and running fine on Mac OS X with RAxML 8.0.29. Please be aware that calling third-party software from within R is a platform-specific process and I cannot guarantee that raxml will behave properly on any system.

References

(in chronological order)

Stamatakis, A., T. Ludwig and H. Meier. 2004. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 1: 1–8.

Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.

Stamatakis, A., P. Hoover, and J. Rougemont. 2008. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 75: 758–771.

Pattengale, N. D., M. Alipour, O. R. P. Bininda-Emonds, B. M. E. Moret, and A. Stamatakis. 2010. How many bootstrap replicates are necessary? Journal of Computational Biology 17: 337-354.

Stamatakis, A. 2014. RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics Advance Access.

See Also

raxml.partitions to store partitioning information in a data frame suitable for input as partitions argument in raxml.

Examples

## bark beetle sequences
data(ips.cox1)
data(ips.16S)
data(ips.28S)

ips <- cbind(ips.cox1, ips.16S, ips.28S,
            fill.with.gaps = TRUE)

exec <- "/Applications/RAxML-code/standard-RAxML/raxmlHPC-PTHREADS-AVX"
w <- sample(1:5, ncol(ips.cox1), replace = TRUE)

## Not run: 

# Simple tree search with GTRCAT and GTRGAMMA
tr <- raxml(ips.cox1, f = "d", N = 2, p = 1234,
           exec = exec) # -1743.528461
tr <- raxml(ips.cox1, m = "GTRGAMMA", f = "d", N = 2, p = 1234,
           exec = exec)
   
# Applying weights to columns                   
tr <- raxml(ips.cox1, f = "d", N = 2, p = 1234,
           weights = w, exec = exec) # -1743.528461

# Rapid bootstrap
tr <- raxml(ips.cox1, m = "GTRGAMMA",
           f = "a", N = 10, p = 1234, x = 1234,
           exec = exec)

# Rapid bootstrap with automatic halt
tr <- raxml(ips.cox1, m = "GTRGAMMA",
           f = "a", N = "autoMRE", p = 1234, x = 1234,
           exec = exec)

## End(Not run)

Partition scheme for RAxML

Description

Given a set of DNA sequence alignments, raxml.partitions creates a data frame with partition bounderies that can be input into raxml.

Usage

raxml.partitions(...)

Arguments

Details

For raxml.partitions to make sense, the DNA sequence alignments must be given exactly in the same order in which they are concatenated into a supermatrix (see Examples section). Without any testing, the type of sequences is supposed to be DNA.

Value

A data frame with four columns (type, locus, begin, and end) and number of rows corresponding to the number of partitions.

See Also

cbind.DNAbin to concatenate multiple alignments; raxml for an interface to RAxML.

Examples

## bark beetle sequences
data(ips.cox1)
data(ips.16S)
data(ips.28S)

## Note the same order of individual
## alignments in both functions:
## ----------------------------
raxml.partitions(cox1 = ips.cox1, 
                 r16S = ips.16S, 
                 r28S = ips.28S)

cbind(ips.cox1, ips.16S, ips.28S,
  fill.with.gaps = TRUE)

XML Input Files for BEAST

Description

Prepare XML files for BEAST with R. BEAST uses an MCMC approach to estimate rooted phylogenies from molecular data (Drummond & Rambaut, 2007).

Usage

rbeauti(
  ...,
  file,
  template = "standard",
  link.clocks = TRUE,
  link.trees = TRUE,
  subst.model,
  clock,
  tree,
  taxonset,
  chain.length = 1e+07,
  log.every = 1000
)

Arguments

Details

rbeauti has been completely rewritten to work with BEAST 2. Currently rbeauti offers few options, because the idea is not to create ready-to-use XML file. That can be done conveniently with BEAUti (the BEAST package's genuine XML generator). Instead, rbeauti is intended to make the definition of large numbers of taxon sets easy. The creation of taxon sets can be done via R scripts and the resulting XML files can be further modified with BEAUti.

References

The XML reference at the BEAST 2 website: http://beast.community/xml_reference Drummond, A.J. & A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 240.

See Also

read.beast, read.beast.table

Examples

data(ips.16S)

## define taxon sets
spec <- rownames(ips.16S)
ingroup <- spec[grep("Ips|Orthomotomicus", spec)]
outgroup <- spec[grep("Pityogenes", spec)]
ts <- list(list(id = "ingroup", taxon = ingroup),
           list(id = "outgroup", taxon = outgroup))

## print XML file to screen
# rbeauti(ips.16S, taxonset = ts)

Reverse-Complement of DNA sequences

Description

Reverse, complement or reverse-complement of DNA sequences.

Usage

rc(seqs, i, complement = TRUE, reverse = TRUE, delete.gaps = FALSE)

Arguments

Value

An object of the same class and dimension as seqs.

Examples

## A minimal sequence alignment:
x <- list(
  seqA = c("a", "a", "c", "c", "g", "t"),
  seqB = c("n", "-", "r", "y", "g", "t"))
x <- as.DNAbin(x)

## Three choices of manipulation:
as.character(x)
as.character(rc(x))                      ## reverse-complement
as.character(rc(x, complement = FALSE))  ## only reverse
as.character(rc(x, reverse = FALSE))     ## only complement

## You can remove gaps:
as.character(rc(x, delete.gaps = TRUE))  ## gaps/indels removed

Reading Sequence Files

Description

Read DNA and amino acid sequences from FASTA, PHILIP, and NEXUS formatted files.

Usage

read.fas(x, text)

read.nex(x)

read.phy(x)

Arguments

Value

An matrix (aligned sequences) or list (unaligned sequences) of class DNAbin or AAbin.

References

Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46: 590-621.

See Also

mafft and prank for sequence alignment, gblocks and aliscore for quality check and cleaning of sequence alignments, cbind.DNAbin for concatenation of sequence alignments.

Examples

## bark beetle COX1 sequences
data(ips.cox1)
## create temporary file names
format <- c(".fas", ".phy", ".nex")
fn <- sapply(format, tempfile, 
             pattern = "ips", tmpdir = tempdir())
## write sequences files
write.fas(ips.cox1, fn[".fas"])
write.phy(ips.cox1, fn[".phy"])
write.nex(ips.cox1, fn[".nex"])
## read sequence files
fas <- read.fas(fn[".fas"])
phy <- read.phy(fn[".phy"])
nex <- read.nex(fn[".nex"])
## remove sequence files
unlink(fn)

Read Bayesian Trees

Description

Thess functions parse chronograms in NEXUS format as produced by TreeAnnotator or output by MrBayes.

Usage

read.mrbayes(file, digits = NULL)

read.beast(file, digits = NULL)

read.starbeast(file)

Arguments

Value

An object of class phylo.

Note

read.starbeast currently parses only skalars and ranges; node statistics with more than two values will be deleted and a warning message will be issued. Future version of read.starbeast will hopefully be able to append list or data frames to phylo objects. If you have any opinion or wishes regarding the question of how this exactly should be managed, send me a message.

read.mrbayes is intended to read single trees with annotated nodes. For reading tree samples from the posterior distribution there is a collection of perl script written by Johan Nylander (https://github.com/nylander/Burntrees).

Author(s)

Christoph Heibl

References

TreeAnnotator: http://beast.community/treeannotator

Metacomments in NEXUS: https://code.google.com/archive/p/beast-mcmc/wikis/NexusMetacommentFormat.wiki

See Also

read.beast.table to extract internal node data from NEXUS file, rbeauti to create XML input for BEAST. HPDbars for plotting highest posterior densities on phylogenies has been moved to package viper.

Extract node data from BEAST chronogram

Description

This function reads a BEAST chronogram such as produced by TreeAnnotator and extracts time, rate, and support values for internal and external nodes. Nodes in the resulting data frame are ordered exactly like in the NEXUS file.

Usage

read.beast.table(file, digits = 2)

Arguments

Value

A matrix; each row corresponds to an internal node, the (ape!)number of which is given in the first column; the remaining columns list the node values extracted from the chronogram.

Author(s)

Christoph Heibl

See Also

read.beast to parse TreeAnnotator output, rbeauti to create XML input for BEAST. HPDbars for plotting highest posterior densities on phylogenies has been moved to package viper.

Identification of Sister Nodes and Clades

Description

For any given internal node in a phylogeny, this function returns the sister clade.

Usage

sister(phy, node, type = "terminal", label = FALSE)

Arguments

Value

A vector of mode "numeric" or "character", containing either tip numbers or labels, respectively.

See Also

descendants, noi.

Examples

# A phylogeny of bark beetles ...
data(ips.tree)
tcol <- rep("black", Ntip(ips.tree))
tcol[ips.tree$tip.label %in% c("Ips_typographus", "Ips_nitidus")] <- "blue"
tcol[ips.tree$tip.label %in% c("Ips_duplicatus")] <- "red"
plot(ips.tree, no.margin = TRUE, tip.color = tcol)
# What is the sister species of Ips typographus?
sister(ips.tree, "Ips_typographus", label = TRUE)
# Return the MRCA of the sister clade of Ips duplicatus
x <- sister(ips.tree, "Ips_duplicatus", "daughter")
nodelabels(node = x, pch = 21, bg = "red")

Find Monophyletic Subsets in Species Lists

Description

Takes a phylogeny and a subset of its tiplabels and splits the list of tiplabels into monophyletic groups (clades).

Usage

splitIntoClades(phy, tips)

Arguments

Value

A list.

Find Pairs of Sister Species

Description

Finds pairs of sister species in a phylogenetic tree.

Usage

terminalSisters(phy, labels = TRUE)

Arguments

Value

A list of which each element contains the tip labels of a sister species pair.

Examples

set.seed(1234)
tr <- rtree(12)
plot(tr)
terminalSisters(tr)

Tip Heights in a Phylogenetic Tree

Description

For each tip (leave, terminal node) in the phylogenetic tree the edge lengths (branch lengths) from root to tip, be it units of time or divergence, is summed up.

Usage

tipHeights(phy)

Arguments

Value

a numeric vector with distances from root to tip for each tip in the phylogenetic tree.

Author(s)

Christoph Heibl

See Also

branching.times

Trait-Dependent Shifts in Molecular Rate

Description

Detection of trait-dependent shifts in the rate of molecular evolution with traitRate (Mayrose & Otto, 2011).

Usage

traitRate(phy, seq, x, mainType = "Optimize_Model", 
   n, charModelParam1 = 0.5, charModelParam2 = 1, 
   gammaParam = 0.5, seqModelParam1 = 2,
   exec = "/Applications/traitRate-1.1/programs/traitRate")

Arguments

Value

Currently none, but look for the output files in the 'RESULTS' subdirectory in the current working directory.

Note

This function is under development!

Author(s)

Christoph Heibl

References

Mayrose, I. & S.P. Otto. 2011. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol. Biol. Evol. 28: 759-770

See Also

read.tree for reading phylogenetic trees, read.fas for reading multiple sequence alignments in FASTA format.

Trim Alignment Ends

Description

Trims both ends of a DNA sequence alignment to the first and last alignment positions that contain a minimum number of IUPAC base characters ("a", "c", "g", "t", "r", "y", "s", "w", "k", "m", "b", "d", "h", "v"). In addition, all gap characters ("-") beyond the first and last base characters of each sequence are replaced by the character "n".

Usage

trimEnds(x, min.n.seq = 4)

Arguments

Value

An object of class DNAbin.

See Also

deleteEmptyCells, deleteGaps

Examples

# simple example alignment:
x <- structure(list(nb = 5, seq = c("acaaggtaca", "-caaggtac-",
"acaaggtaca", "aca--gtaca", "-ccaggta--"), nam = LETTERS[1:5]),
.Names = c("nb", "seq", "nam"), class = "alignment")
# convert to DNAbin:
x <- as.DNAbin(x)
# fill missing nucleotides:
x <- trimEnds(x)
# show results:
as.character(x[2, ])

Unlist To First Level Only

Description

Does the same as unlist, but recurses only one level.

Usage

unlistFirstLevel(z, use.names = TRUE)

Arguments

Write DNA Sequences to File

Description

Write DNA sequences and morphological data to FASTA, PHYLIP, or NEXUS formatted files.

Usage

	
write.fas(x, file, block.width = FALSE, 
    truncate = FALSE, append = FALSE)

write.phy(x, file, block.width = FALSE, 
    strict = FALSE)

write.nex(x, file, block.width = 60, 
    taxblock = FALSE)

Arguments

Details

write.nex can handle multiple DNA sequence alignments, which are handed over as a list of objects of class DNAbin. Correct matching of the rows in the alignments is cared for automatically, hence the individual alignments can contain different numbers of samples and samples need not be in the same order.

Value

None, except when called with file left unspecified, which causes the file content to be returned as a vector of mode "character". This is particularly useful for constructing special types of input files, e.g. for MrBayes (mrbayes).

Author(s)

Christoph Heibl

References

Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46: 590-621.

See Also

read.fas, read.phy, and read.nex for reading of DNA sequence files.

Examples

data(ips.cox1)
data(ips.28S)

## Examples for FASTA files
## ------------------------
write.fas(ips.cox1[1:5, 1:120], block.width = 60)

## Examples for PHYLIP files
## ------------------------
write.phy(ips.cox1[1:5, 1:20], block.width = 40)

## Examples for NEXUS files
## ------------------------
x <- list(cox1 = ips.cox1[1:5, 1:10], 
          rna28S = ips.28S[1:5, 1:30])
write.nex(x, block.width = 20)

# Truncation of taxonnames:
# -------------------------
rownames(ips.cox1)[1] <- "AVeeeeeeeeeeeeeeeeeryLongName"
write.fas(ips.cox1, truncate = 10)

# If truncation leads to identical taxonnames,
# a warning will be issued:
# -------------------------
rownames(ips.cox1)[1:2] <- "AVeeeeeeeeeeeeeeeeeryLongName"
write.fas(ips.cox1, truncate = 10)