| Title: | Basic functions for phylogenetic analysis |
|---|---|
| Description: | This package provides functions to read, write, manipulate, estimate, and summarize phylogenetic trees including species trees which contain not only the topology and branch lengths but also population sizes. The input/output functions can read tree files in which trees are presented in parenthetic format. The trees are read in as a string and then transformed to a matrix which describes the relationship of nodes and branch lengths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between NEXUS and PHYLIP. Some basic functions have already been established in the package for manipulating trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consensus", "coaltime, "popsize", "treedist" for summarizing phylogenetic trees, calculating the coalescence time, population size, and tree distance. The function maxtree is built in the package to esimtate the species tree from multiple gene trees. |
| Authors: | Liang Liu |
| Maintainer: | Liang Liu <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1 |
| Built: | 2024-11-05 03:26:08 UTC |
| Source: | https://github.com/cran/phybase |
This package provides functions to read, write, manipulate, estimate, and summarize phylogenetic trees including species trees which contains not only the topology and branch lengths but also population sizes. The input/output functions can read tree files in which trees are presented in parenthetic format. The trees are read in as a string and then transformed to a matrix which describes the relationship of nodes and branch lengths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between NEXUS and PHYLIP. Some basic functions have already been established in the package for manipulating trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consensus", "coaltime, "popsize", "treedist" for summarizing phylogenetic trees, calculating the coalescence time, population size, and tree distance. The function maxtree is built in the package to esimtate the species tree from multiple gene trees.
| Package: | PhyBase |
| Type: | Package |
| Version: | 1.1 |
| Date: | 2008-03-25 |
| License: | GPL (>=2.0.0) |
Liang Liu
Maintainer: Liang Liu <[email protected]>
This function returns the ancestors of a node and their divergence times.
ancandtime(inode, nodematrix, nspecies)ancandtime(inode, nodematrix, nspecies)
inode |
a node in the tree. |
nodematrix |
the tree matrix. |
nspecies |
number of species (taxa) in the tree. |
Liang Liu
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes inode<-6 ancandtime(inode,nodematrix,nspecies=5)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes inode<-6 ancandtime(inode,nodematrix,nspecies=5)
The function returns the ancestral nodes of inode including inode itself.
ancestor(inode, nodematrix)ancestor(inode, nodematrix)
inode |
the node number |
nodematrix |
the tree node matrix. it must be a rooted tree. |
The function returns a vector of ancestoral nodes of inode including inode itself.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes ancestor(6,nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes ancestor(6,nodematrix)
This function can be used to bootstrap sequences.
bootstrap(sequence)bootstrap(sequence)
sequence |
sequence matrix. |
In the sequences matrix, the columns are "Taxa" and the rows are "sites". The function will bootstrap the rows.
the function returns a sequence matrix with sites randomly sampled from the original matrix with replacement.
Liang Liu
#construct the DNA sequences of three taxa seq <- matrix("A",ncol=4,nrow=3) rownames(seq)<-c("taxa1","taxa2","taxa3") seq[,2]<-"G" seq[,3]<-"C" seq[,4]<-"T" bootstrap(seq)#construct the DNA sequences of three taxa seq <- matrix("A",ncol=4,nrow=3) rownames(seq)<-c("taxa1","taxa2","taxa3") seq[,2]<-"G" seq[,3]<-"C" seq[,4]<-"T" bootstrap(seq)
The function bootstraps sequence columns for each locus sampled from the original multilocus data. It consists of two step. First, it bootstraps loci. Then it bootstraps sequences for each locus.
bootstrap.mulgene(sequence,gene,name,boot,outfile="")bootstrap.mulgene(sequence,gene,name,boot,outfile="")
sequence |
data matrix |
gene |
location of each locus |
name |
taxa names of sequences |
boot |
the number of bootstrap samples |
outfile |
output file |
In the sequences matrix, the rows are "Taxa" and the columns are "sites".
The function generates a data file in phylip format.
Liang Liu [email protected]
#construct the DNA sequences of three taxa seq <- matrix("A",ncol=4,nrow=3) rownames(seq)<-c("taxa1","taxa2","taxa3") seq[,2]<-"G" seq[,3]<-"C" seq[,4]<-"T" name<-rownames(seq) #taxa names of the sequences #construct two loci. The first two nucleotides represent the first locus, while nucleotide 3 and 4 represent the second locus. gene<-matrix(0,ncol=2,nrow=2) gene[1,]<-c(1,2) gene[2,]<-c(3,4) gene bootstrap.mulgene(seq,gene,name,boot=2,outfile="bootdata.txt") #the output file is saved at "bootdata.txt"#construct the DNA sequences of three taxa seq <- matrix("A",ncol=4,nrow=3) rownames(seq)<-c("taxa1","taxa2","taxa3") seq[,2]<-"G" seq[,3]<-"C" seq[,4]<-"T" name<-rownames(seq) #taxa names of the sequences #construct two loci. The first two nucleotides represent the first locus, while nucleotide 3 and 4 represent the second locus. gene<-matrix(0,ncol=2,nrow=2) gene[1,]<-c(1,2) gene[2,]<-c(3,4) gene bootstrap.mulgene(seq,gene,name,boot=2,outfile="bootdata.txt") #the output file is saved at "bootdata.txt"
The function changes the tree root.
change.root(nodematrix, newroot)change.root(nodematrix, newroot)
nodematrix |
the tree node matrix |
newroot |
the node number of the new root |
The function always returns an unrooted tree. Use the function link{root.tree} to root the unrooted tree if you need a rooted tree.
nodes |
the tree node matrix after changing the tree root |
rootnode |
the node number of the new root |
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes change.root(nodematrix,6)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes change.root(nodematrix,6)
For a given set of gene trees, the UPGMA tree is constructed from the distance matrix based on the average coalescence times among taxa.
coal.sptree(trees, speciesname, nspecies, outgroup=1)coal.sptree(trees, speciesname, nspecies, outgroup=1)
trees |
a vector of trees in newick format |
speciesname |
species names |
nspecies |
number of species |
outgroup |
the node number of the species used to root the tree |
If the gene trees are not clocklike trees, they are first converted to clock trees using function noclock2clock and then construct a distance matrix in which the entries are twice the coalescence times among species. The distance matrix is used to build an UPGMA tree as the estimate of the species tree. This function is different from steac.sptree in that steac.sptree uses nucleotide distances to construct distance matrix.
The function returns the tree node matrix and the estimate of the species tree.
Liang Liu
See also to steac.sptree
data(rooted.tree) genetrees<-rooted.tree spname<-species.name(genetrees[1]) coal.sptree(genetrees,spname,nspecies=4,outgroup=4)data(rooted.tree) genetrees<-rooted.tree spname<-species.name(genetrees[1]) coal.sptree(genetrees,spname,nspecies=4,outgroup=4)
The function computes the coalescence time of two nodes.
coaltime(inode, jnode, nodematrix, nspecies)coaltime(inode, jnode, nodematrix, nspecies)
inode |
the first node, it could be an internode. |
jnode |
the second node, it could be an internode. |
nodematrix |
the tree node matrix |
nspecies |
the number of species |
the function returns the coalescence time of inode and jnode.
Liang Liu
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" taxaname<-species.name(treestr) nodematrix<-read.tree.nodes(treestr,name=taxaname)$nodes coaltime(1,2,nodematrix,5) #the coalescence time of taxa H (1) and C (2).treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" taxaname<-species.name(treestr) nodematrix<-read.tree.nodes(treestr,name=taxaname)$nodes coaltime(1,2,nodematrix,5) #the coalescence time of taxa H (1) and C (2).
The function returns a consensus tree from multiple gene trees.
consense(treestr, name,type="freq")consense(treestr, name,type="freq")
treestr |
a vector of tree strings |
name |
the species names |
type |
if type="freq", the frequency of each clade in the consensus tree is presented at the node of the clade. if type="prop", the proportion of each clade is presented at the node of the clade" |
The function returns the consensus tree and species names.
Liang Liu [email protected]
treestr<-c("((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);","((((H:0.00402,G:0.00402):0.00304,C:0.00707):0.00929,O:0.01635):0.1,W:0.12);","((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);") name<-species.name(treestr[1]) consense(treestr,name) ###unrooted trees data(unrooted.tree) name<-paste("S",1:29,sep="") consense(unrooted.tree,name)treestr<-c("((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);","((((H:0.00402,G:0.00402):0.00304,C:0.00707):0.00929,O:0.01635):0.1,W:0.12);","((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);") name<-species.name(treestr[1]) consense(treestr,name) ###unrooted trees data(unrooted.tree) name<-paste("S",1:29,sep="") consense(unrooted.tree,name)
This function deletes a node (and its descendant nodes) from the tree.
del.node(inode, name, nodematrix)del.node(inode, name, nodematrix)
inode |
the node to be deleted |
name |
the species names |
nodematrix |
the tree node matrix |
The species names are those defined in the original tree before deleting the node inode. No need to delete the species name of inode! If inode is an internode, the whole subtree below inode will be deleted.
nodes |
the tree node matrix after deleting |
treestr |
the tree string of the tree after deleting |
Liang Liu
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" spname<-read.tree.nodes(treestr)$names nodematrix<-read.tree.nodes(treestr)$nodes del.node(6,spname,nodematrix) ##unrooted tree data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes name<-paste("S",1:29,sep="") del.node(6,name,nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" spname<-read.tree.nodes(treestr)$names nodematrix<-read.tree.nodes(treestr)$nodes del.node(6,spname,nodematrix) ##unrooted tree data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes name<-paste("S",1:29,sep="") del.node(6,name,nodematrix)
This function constructs gene tree vectors from gene trees across loci. The gene tree vectors can be used to construct maximum tree by the function maxtree.
genetree.vector(filenames,outputfile)genetree.vector(filenames,outputfile)
filenames |
the gene tree files |
outputfile |
the output file |
The function returns a matrix of gene trees. Each row represents a gene tree vector. The gene tree vector consists of trees from multiple gene tree files.
Liang Liu [email protected]
Liu, L. and D.K. Pearl. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 2007, 56:504-514.
Edwards, S.V., L. Liu., and D.K. Pearl. High resolution species trees without concatenation. PNAS, 2007, 104:5936-5941.
This function can get gene coalescence times in the species tree.
getcoaltime(genetree, sptree, ntax, nspecies, species.structure)getcoaltime(genetree, sptree, ntax, nspecies, species.structure)
genetree |
a genetree matrix |
sptree |
a species tree matrix |
ntax |
number of taxa in the gene tree |
nspecies |
number of species in the species tree |
species.structure |
sequence-species relationship |
The function returns a two-column matrix, the first column is the ancestral node in the species tree, the second column is the gene coalescence time at the corresponding ancestral node in the species tree.
Liang Liu
genetree<-"(((A:1,B:1):3,C:4):2,D:6);" sptree<-"(((A:0.5,B:0.5):1,C:1.5):1,D:2.5);" name<-c("A","B","C","D") genetree<-read.tree.nodes(genetree,name)$nodes sptree<-read.tree.nodes(sptree,name)$nodes ntax<-length(name) nspecies<-length(name) species.structure<-matrix(0,nrow=nspecies,ncol=ntax) diag(species.structure)<-1 getcoaltime(genetree,sptree,ntax,nspecies,species.structure)genetree<-"(((A:1,B:1):3,C:4):2,D:6);" sptree<-"(((A:0.5,B:0.5):1,C:1.5):1,D:2.5);" name<-c("A","B","C","D") genetree<-read.tree.nodes(genetree,name)$nodes sptree<-read.tree.nodes(sptree,name)$nodes ntax<-length(name) nspecies<-length(name) species.structure<-matrix(0,nrow=nspecies,ncol=ntax) diag(species.structure)<-1 getcoaltime(genetree,sptree,ntax,nspecies,species.structure)
This is an internal function for calculating the rannala and yang's formula
This function checks the tree to see if the branch lengths satisfy the molecular clock assumption. For each node, the lengths of the left lineage and right lineage are compared. If they are not equal to each other and the difference is greater than threshold, the function will return FALSE. This function does not perform statistical test for the molecular clock assumption.
is.clock(nodematrix, nspecies,threshold)is.clock(nodematrix, nspecies,threshold)
nodematrix |
the tree node matrix |
nspecies |
the number of species |
threshold |
the critical value for the difference between the length of the left decendant lineage and that of the right decendant lieage of an internode. The difference below the threshold is treated as no difference. |
The function returns TRUE for a clock tree and FALSE for a non-clock tree.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes ##if the threshold is set to be large, the tree is a clock tree is.clock(nodematrix,5,0.0001) ##[1] TRUE ##if the threshold is a small number, the tree is not a clock tree. is.clock(nodematrix,5,0.00001) ##[1] FALSEtreestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes ##if the threshold is set to be large, the tree is a clock tree is.clock(nodematrix,5,0.0001) ##[1] TRUE ##if the threshold is a small number, the tree is not a clock tree. is.clock(nodematrix,5,0.00001) ##[1] FALSE
This function can test if the tree is rooted.
is.rootedtree(tree)is.rootedtree(tree)
tree |
tree string or tree node matrix |
The function returns TRUE if the tree is a rooted tree. Otherwise, it returns FALSE.
Liang Liu [email protected]
data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes is.rootedtree(nodematrix) data(rooted.tree) is.rootedtree(rooted.tree[1])data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes is.rootedtree(nodematrix) data(rooted.tree) is.rootedtree(rooted.tree[1])
The function computes the Maximum Tree from multiple gene trees.
maxtree(genetreevector,spname,taxaname,species.structure)maxtree(genetreevector,spname,taxaname,species.structure)
genetreevector |
a vector of gene trees |
spname |
the species names |
taxaname |
the names of taxa |
species.structure |
the correspondence between species and taxa |
The function returns the node matrix and tree string of the maximum tree. It also returns the species names.
Liang Liu [email protected]
Liu, L. and D.K. Pearl. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 2007, 56:504-514.
Edwards, S.V., L. Liu., and D.K. Pearl. High resolution species trees without concatenation. PNAS, 2007, 104:5936-5941.
genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);","((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"); species.structure<-matrix(0,5,5) diag(species.structure)<-1 name<-species.name(genetreevector[1]) maxtree(genetreevector,name,name,species.structure)genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);","((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"); species.structure<-matrix(0,5,5) diag(species.structure)<-1 name<-species.name(genetreevector[1]) maxtree(genetreevector,name,name,species.structure)
The function can find the most recent common ancestor of two nodes inode and jnode
mrca.2nodes(inode, jnode, nodematrix)mrca.2nodes(inode, jnode, nodematrix)
inode |
the node |
jnode |
the node |
nodematrix |
the tree node matrix |
anc |
the node number of the most recent common ancestor of |
dist |
the distance between the two nodes. |
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes mrca.2nodes(1,2,nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes mrca.2nodes(1,2,nodematrix)
The function can find the most recent common ancestor of multiple nodes specified in nodevector
mrca.nodes(nodevector, nodematrix)mrca.nodes(nodevector, nodematrix)
nodevector |
a set of nodes |
nodematrix |
the tree node matrix |
The function returns the node number of the most recent common ancestor of the nodes in nodevector.
Liang Liu [email protected]
mrca.2nodes, coaltime, popsize
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes mrca.nodes(c(1,2,3),nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes mrca.nodes(c(1,2,3),nodematrix)
In the non-clock species tree model (Liu, et.al), the lineages (populations) in the species tree are allowed to have variable mutation rates. This function is used to simulate mutation rates for the non-clock species tree model. There are many other ways to simulate variable mutation rates across populations in the species tree.
mutation_exp(sptree, root, inode, nspecies,alpha)mutation_exp(sptree, root, inode, nspecies,alpha)
sptree |
the species tree matrix |
root |
the root of the species tree |
inode |
the root of the species tree |
nspecies |
the number of species in the species tree |
alpha |
the parameter in the gamma distribution used to generate mutation rates. |
mutation rates are generated from gamma (alpha, alpha/w) where w is the mutation rate of the parent population of the current node. Thus the mean of the mutation rate of the current node equals to the mutation rate of its parent population.
The function returns a species tree matrix with mutation rates in the last column.
Liang Liu
sptree<-"((((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01):0.1#0.01,W:0.12#0.01);" nodematrix<-read.tree.nodes(sptree)$nodes mutation_exp(nodematrix, root=9, inode=9, nspecies=5, alpha=5)sptree<-"((((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01):0.1#0.01,W:0.12#0.01);" nodematrix<-read.tree.nodes(sptree)$nodes mutation_exp(nodematrix, root=9, inode=9, nspecies=5, alpha=5)
This function replaces the species names in the tree string with their node numbers.
name2node(treestr,name="")name2node(treestr,name="")
treestr |
the tree string |
name |
the species names |
If species names are not given, the function will use the sorted species names in the tree string.
The function returns the tree string with the species names replaced by the node numbers.
Liang Liu [email protected]
treestr<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" name<-c("H","G", "C", "O") name2node(treestr,name)treestr<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" name<-c("H","G", "C", "O") name2node(treestr,name)
This function converts a non-clocklike tree to a clocklike tree using an ad-hoc approach described in the paper Liu et al 2007.
noclock2clock(inode, treematrix, nspecies)noclock2clock(inode, treematrix, nspecies)
inode |
root of the tree |
treematrix |
tree node matrix |
nspecies |
the number of species in the tree |
The function returns the tree node matrix of the clocklike tree.
Liang Liu
~put references to the literature/web site here ~
treestr<-"(((H:1,C:3):2,G:6):2,O:10);" name<-species.name(treestr) treenode<-read.tree.nodes(treestr,name)$nodes noclock2clock(7,treenode,4)treestr<-"(((H:1,C:3):2,G:6):2,O:10);" name<-species.name(treestr) treenode<-read.tree.nodes(treestr,name)$nodes noclock2clock(7,treenode,4)
The function calculates the height of a node. The tree is assumed to be an ultramatric tree.
node.height(inode, nodematrix, nspecies)node.height(inode, nodematrix, nspecies)
inode |
the node number |
nodematrix |
the tree node matrix |
nspecies |
the number of species in the tree |
The function returns the height of inode.
Liang Liu [email protected]
tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" nodematrix<-read.tree.nodes(tree.string)$nodes node.height(6,nodematrix,4)tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" nodematrix<-read.tree.nodes(tree.string)$nodes node.height(6,nodematrix,4)
This function replaces node numbers in a tree string by species names.
node2name(treestr,name="")node2name(treestr,name="")
treestr |
a tree string |
name |
species names |
The function returns the tree string with the node numbers replaced by the species names.
Liang Liu
treestr<-"(((1:4.2,2:4.2):3.1,3:7.3):6.3,4:13.5);" name<-c("H","C", "G", "O") node2name(treestr,name)treestr<-"(((1:4.2,2:4.2):3.1,3:7.3):6.3,4:13.5);" name<-c("H","C", "G", "O") node2name(treestr,name)
The function returns the offspring nodes of inode.
offspring.nodes(inode, nodematrix, nspecies)offspring.nodes(inode, nodematrix, nspecies)
inode |
the node of which the the offspring nodes will be found by the function. |
nodematrix |
the tree node matrix. |
nspecies |
the number of species. |
The function returns the offspring nodes of inode.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes offspring.nodes(7,nodematrix,5)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes offspring.nodes(7,nodematrix,5)
The function returns a string of offspring nodes of inode.
offspring.nodes.string(inode, nodematrix, nspecies)offspring.nodes.string(inode, nodematrix, nspecies)
inode |
the node of which the the offspring nodes will be found by the function. |
nodematrix |
the tree node matrix |
nspecies |
the number of species |
The function returns a string of offspring nodes of inode.
Liang Liu [email protected]
The function returns the descendant species of inode.
offspring.species(inode, nodematrix, nspecies)offspring.species(inode, nodematrix, nspecies)
inode |
the node. |
nodematrix |
the tree node matrix |
nspecies |
the number of species |
This function returns the descendant species of inode, while the function offspring.nodes returns all the descendant nodes of inode including internal nodes in the tree.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes offspring.species(7,nodematrix,5)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes offspring.species(7,nodematrix,5)
The function computes all pairwise distances among taxa in the tree.
pair.dist(nodematrix, nspecies)pair.dist(nodematrix, nspecies)
nodematrix |
the tree node matrix |
nspecies |
the number of taxa in the tree |
The function returns a distance matrix.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes pair.dist(nodematrix,5)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes pair.dist(nodematrix,5)
Calculate pairwise distances among DNA sequences. The DNA sequences are coded as 1:A, 2:G, 3:C, 4:T.
pair.dist.dna(sequences, nst = 0)pair.dist.dna(sequences, nst = 0)
sequences |
DNA sequences |
nst |
substitution model. 0:no model, 1:JC |
If nst=0, the distance is equal to the proportion of sites having different nucleotides between two sequences.
The function returns a distance matrix.
Liang Liu [email protected]
Jukes, TH and Cantor, CR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
tree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;" nodematrix<-read.tree.nodes(tree)$nodes sequences<-sim.dna(nodematrix,10000,model=1) pair.dist.dna(sequences,nst=1)tree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;" nodematrix<-read.tree.nodes(tree)$nodes sequences<-sim.dna(nodematrix,10000,model=1) pair.dist.dna(sequences,nst=1)
If some species have multiple taxa, the pairwise distance between two species is equal to the average of the distances between all pairs of taxa in the two species. This functions returns the pairwise distances among species (average over all taxa in the species).
pair.dist.mulseq(dist, species.structure)pair.dist.mulseq(dist, species.structure)
dist |
the distance matrix of taxa |
species.structure |
a matrix with rows representing species and columns representing taxa. 1: the species (row) has the taxon at the corresponding column. see the example. |
This functions returns the distance matrix of species.
Liang Liu
See Also as pair.dist
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes dist<-pair.dist(nodematrix,5) species.structure<-matrix(0,nrow=2,ncol=5) #2 species and 5 taxa species.structure[1,]<-c(1,1,1,0,0) #taxa 1,2,3 belong to the first species species.structure[2,]<-c(0,0,0,1,1) #taxa 4,5 belong to the second species pair.dist.mulseq(dist,species.structure)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes dist<-pair.dist(nodematrix,5) species.structure<-matrix(0,nrow=2,ncol=5) #2 species and 5 taxa species.structure[1,]<-c(1,1,1,0,0) #taxa 1,2,3 belong to the first species species.structure[2,]<-c(0,0,0,1,1) #taxa 4,5 belong to the second species pair.dist.mulseq(dist,species.structure)
partition a tree.
partition.tree(tree,nspecies)partition.tree(tree,nspecies)
tree |
the tree node matrix |
nspecies |
the number of species |
The function returns a matrix. Each row represents a particular partition of the tree. The position of "1" in the matrix indicates the presence of the corresponding species in the partition. The last number at each row is the frequency of that partition. This function returns the partition matrix for only one tree. For multiple trees, the partitions and their frequencies can be obtained by the function consense.
Liang Liu
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes partition.tree(nodematrix,5) # # [,1] [,2] [,3] [,4] [,5] [,6] #[1,] 1 0 1 0 0 1 #[2,] 1 1 1 0 0 1 #[3,] 1 1 1 1 0 1 # #The last number of each row is the frequency of the corresponding partition. For example, the frequency of the #first partition (1 0 1 0 0) is 1. The first partition includes species 1 and 3 as indicated by the position of 1 in the partition. #Each row represens a partition and its frequency.treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes partition.tree(nodematrix,5) # # [,1] [,2] [,3] [,4] [,5] [,6] #[1,] 1 0 1 0 0 1 #[2,] 1 1 1 0 0 1 #[3,] 1 1 1 1 0 1 # #The last number of each row is the frequency of the corresponding partition. For example, the frequency of the #first partition (1 0 1 0 0) is 1. The first partition includes species 1 and 3 as indicated by the position of 1 in the partition. #Each row represens a partition and its frequency.
The function plots phylogenetic trees.
plottree(tree)plottree(tree)
tree |
a phylogenetic tree in newrick format |
use the function "plot.phylo" in package APE to plot phylogenetic trees.
write.subtree, read.tree.string
treestr<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" plottree(treestr)treestr<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" plottree(treestr)
This function computes the population size of the most recent common ancestor of two nodes.
popsize(inode, jnode, nodematrix)popsize(inode, jnode, nodematrix)
inode |
the first node, it could be an internode. |
jnode |
the second node, it could be an internode. |
nodematrix |
the tree node matrix |
The function returns the population size of the most recent common ancestor of inode and jnode.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402#0.035):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes popsize(1,2,nodematrix) #[1] -9 ##this tree does not have values for population size. popsize(1,1,nodematrix) #[1] 0.035 ##the population size for the species C is 0.035treestr<-"((((H:0.00402,C:0.00402#0.035):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" nodematrix<-read.tree.nodes(treestr)$nodes popsize(1,2,nodematrix) #[1] -9 ##this tree does not have values for population size. popsize(1,1,nodematrix) #[1] 0.035 ##the population size for the species C is 0.035
This function changes branch lengths of a gene tree with the mutation rates in the species tree.
populationMutation(sptree, spnodedepth, genetree, genenodedepth, speciesmatrix)populationMutation(sptree, spnodedepth, genetree, genenodedepth, speciesmatrix)
sptree |
the species tree |
spnodedepth |
depth of the species tree |
genetree |
a gene tree |
genenodedepth |
depth of the gene tree |
speciesmatrix |
tree node matrix of the species tree |
It returns a gene tree.
Liang Liu
The function summarize a set of trees by calculating the proportion of each tree in the tree set.
postdist.tree(trees,name)postdist.tree(trees,name)
trees |
a vector of tree strings |
name |
the species names |
trees |
a vector of tree |
prob |
the probability associated with each tree in the vector |
Liang Liu [email protected]
See Also as read.tree.nodes
library(phybase) tree<-"(((H:0.005 , C:0.005 ) : 0.00025 #.01, G:0.00525):0.00025 #0.01 , O:0.0055) #.01;" name<-species.name(tree) nodematrix<-read.tree.nodes(tree,name)$nodes rootnode<-7 seq<-rep(1,4) nsim<-100 str<-rep(0,nsim) for(i in 1:nsim){ str[i]<-sim.coaltree.sp(rootnode,nodematrix,4,seq,name=name)$gt } postdist.tree(str,name)library(phybase) tree<-"(((H:0.005 , C:0.005 ) : 0.00025 #.01, G:0.00525):0.00025 #0.01 , O:0.0055) #.01;" name<-species.name(tree) nodematrix<-read.tree.nodes(tree,name)$nodes rootnode<-7 seq<-rep(1,4) nsim<-100 str<-rep(0,nsim) for(i in 1:nsim){ str[i]<-sim.coaltree.sp(rootnode,nodematrix,4,seq,name=name)$gt } postdist.tree(str,name)
The function returns the rank of each node in the tree.
rank.nodes(treenode, inode, ntaxa, start, rank)rank.nodes(treenode, inode, ntaxa, start, rank)
treenode |
tree node matrix |
inode |
the tree root |
ntaxa |
the number of taxa in the tree |
start |
the maximum rank |
rank |
a dummy vector |
The function returns a vector of ranks for the nodes in the tree.
Liang Liu [email protected]
This function calculates the likelihood of a vector of gene trees given the species tree using the Rannala and Yang's formula
rannalandyang(gtree, stree, taxaname,spname,species.structure)rannalandyang(gtree, stree, taxaname,spname,species.structure)
gtree |
a collection of gene trees |
stree |
a species tree in newick format |
taxaname |
the names of taxa |
spname |
the names of species |
species.structure |
define which sequence belong to which species |
The function returns the log likelihood score.
Liang Liu
Rannala, B. and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
gtree<-"(((A:1,B:1):3,C:4):2,D:6);" stree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;" taxaname<-c("A","B","C","D") spname<-taxaname ntax<-length(taxaname) nspecies<-length(spname) species.structure<-matrix(0,nrow=nspecies,ncol=ntax) diag(species.structure)<-1 rannalandyang(gtree,stree,taxaname,spname,species.structure)gtree<-"(((A:1,B:1):3,C:4):2,D:6);" stree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;" taxaname<-c("A","B","C","D") spname<-taxaname ntax<-length(taxaname) nspecies<-length(spname) species.structure<-matrix(0,nrow=nspecies,ncol=ntax) diag(species.structure)<-1 rannalandyang(gtree,stree,taxaname,spname,species.structure)
This function can generate random numbers from a dirichlet distribution.
rdirichlet(n,a)rdirichlet(n,a)
n |
the number of random numbers to be generated |
a |
shape parameters of the dirichlet distribution |
The function returns random numbers from a dirichlet distribution.
Code is taken from Greg's Miscellaneous Functions (gregmisc). His code was based on code posted by Ben Bolker to R-News on Fri Dec 15 2000.
rdirichlet(1,c(3,3,3))rdirichlet(1,c(3,3,3))
The function reads sequences from files in the nexus or phylip format.
read.dna.seq(file="", format="nexus")read.dna.seq(file="", format="nexus")
file |
the input file name |
format |
nexus or phylip |
seq |
sequences |
gene |
partitions on the sequences. Each partition represents a gene or a locus. |
Liang Liu
Read a tree string in parenthesic format and output tree nodes, species names and whether the tree is rooted
read.tree.nodes(str, name = "")read.tree.nodes(str, name = "")
str |
a tree string in the parenthetical format |
name |
species names |
This function reads a tree string into a matrix that describes the relationships among nodes and corresponding branch lengths. Each row in the matrix represents a node. The first n rows contain the information of the nodes at the tips of the tree. The order of the first n nodes is identical to the alphabetic order of the species names given by name. If name is null, the names will be extracted from the tree str and the first n nodes are in the same order as the species names appear in the tree str from left to right.
The numbers after ":" are branch lengths. The numbers after pound signs are population sizes. The numbers after "
nodes |
nodes is a matrix that describes the relationships among nodes and corresponding branch lengths and population sizes if the tree is a species tree. Each row corresponds a node in the tree. The matrix has 5 columns. The first column is the father of the current node. The following columns are left son, right son, branch length, and population size. The value -9 implies that the information does not exist. The last row is the root of the tree. If the tree is unrooted, the first number of the root node is -8, while it is -9 for a rooted tree. |
names |
species names in the same order of the first n nodes. |
root |
TRUE for a rooted tree, FALSE for an unrooted tree. |
Liang Liu [email protected]
read.tree.string, species.name
##read an unrooted tree data(unrooted.tree) tree<-read.tree.nodes(unrooted.tree[1]) tree$nodes tree$names tree$root #read a rooted tree data(rooted.tree) tree<-read.tree.nodes(rooted.tree[1]) tree$nodes tree$names tree$root##read an unrooted tree data(unrooted.tree) tree<-read.tree.nodes(unrooted.tree[1]) tree$nodes tree$names tree$root #read a rooted tree data(rooted.tree) tree<-read.tree.nodes(rooted.tree[1]) tree$nodes tree$names tree$root
This function reads tree strings in the parenthetical format from a tree file. The output of the function is a vector of tree strings that can be converted to a matrix of nodes by the function read.tree.nodes.
read.tree.string(file = "", format="nexus")read.tree.string(file = "", format="nexus")
file |
the tree file that contains trees in the parenthetical format. |
format |
phylip or nexus |
The function can read NEXUS and PHYLIP tree files. It works for other types of tree files as long as the trees in the tree files are parenthetical trees. This function combining with write.tree.string can change the tree file format.
tree |
a vector of tree strings. |
names |
species names. |
root |
TRUE for rooted trees, FALSE for unrooted trees |
Liang Liu [email protected]
write.tree.string, read.tree.nodes
##read rooted trees in PHYLIP format cat("(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);",file = "phylip.tre", sep = "\n") tree.string<-read.tree.string("phylip.tre") tree.string ##read unrooted trees in NEXUS format cat("#NEXUS [ID: 4045516090] begin trees; translate 1 WW_7A03_1, 2 WW_7H06_2, 3 WW_7H05_1, 4 WW_N03__5, 5 WW_Snnr_1, 6 WW_7P10__1, 7 WW_7A05_1, 8 WW_B03__1, 9 WW_B04_1, 10 WW_D07_9, 11 WW_7K01_1, 12 WW_7K04_1, 13 WW_7N13_1, 14 WW_M02_1, 15 WW_N04_1, 16 WW_UK6_1, 17 WW_7A04_1, 18 Pfuscatus_PF2_4, 19 Pfuscatus_PF1_1, 20 Pfuscatus_PF3_2, 21 PCabietinus_331_1, 22 PCabietinus_333_6, 23 PCabietinus_336_1, 24 PCcollybita_GB_1, 25 PCtristis_GB_1, 26 PCbrehmii_GB_1, 27 Psibilatrix_GB_1, 28 Pbonelli_GB_1, 29 PTviridanus_1; tree rep.1 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); tree rep.100 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); tree rep.200 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); end;",file="tree.nexus") tree.string<-read.tree.string("tree.nexus") tree.string##read rooted trees in PHYLIP format cat("(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);",file = "phylip.tre", sep = "\n") tree.string<-read.tree.string("phylip.tre") tree.string ##read unrooted trees in NEXUS format cat("#NEXUS [ID: 4045516090] begin trees; translate 1 WW_7A03_1, 2 WW_7H06_2, 3 WW_7H05_1, 4 WW_N03__5, 5 WW_Snnr_1, 6 WW_7P10__1, 7 WW_7A05_1, 8 WW_B03__1, 9 WW_B04_1, 10 WW_D07_9, 11 WW_7K01_1, 12 WW_7K04_1, 13 WW_7N13_1, 14 WW_M02_1, 15 WW_N04_1, 16 WW_UK6_1, 17 WW_7A04_1, 18 Pfuscatus_PF2_4, 19 Pfuscatus_PF1_1, 20 Pfuscatus_PF3_2, 21 PCabietinus_331_1, 22 PCabietinus_333_6, 23 PCabietinus_336_1, 24 PCcollybita_GB_1, 25 PCtristis_GB_1, 26 PCbrehmii_GB_1, 27 Psibilatrix_GB_1, 28 Pbonelli_GB_1, 29 PTviridanus_1; tree rep.1 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); tree rep.100 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); tree rep.200 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000); end;",file="tree.nexus") tree.string<-read.tree.string("tree.nexus") tree.string
Root a tree.
root.tree(nodematrix,outgroup)root.tree(nodematrix,outgroup)
nodematrix |
the tree node matrix |
outgroup |
the node used as outgroup |
The function returns a rooted tree.
Liang Liu [email protected]
data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes root.tree(nodematrix,23)data(unrooted.tree) nodematrix<-read.tree.nodes(unrooted.tree[1])$nodes root.tree(nodematrix,23)
An example of rooted trees
data(rooted.tree)data(rooted.tree)
Liang Liu [email protected]
data(rooted.tree) read.tree.nodes(rooted.tree[1])data(rooted.tree) read.tree.nodes(rooted.tree[1])
This function can be used to find the root of a tree.
rootoftree(nodematrix)rootoftree(nodematrix)
nodematrix |
the tree node matrix |
The function returns the root of the tree.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names rootoftree(nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names rootoftree(nodematrix)
The function computes the shallowest coalescence tree from multiple gene trees.
sctree(genetreevector,spname,taxaname,species.structure)sctree(genetreevector,spname,taxaname,species.structure)
genetreevector |
a vector of gene trees |
spname |
the species names |
taxaname |
the names of taxa |
species.structure |
the correspondence between species and taxa |
The function returns the node matrix and tree string of the maximum tree. It also returns the species names.
Liang Liu [email protected]
Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);","((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"); species.structure<-matrix(0,5,5) diag(species.structure)<-1 name<-species.name(genetreevector[1]) sctree(genetreevector,name,name,species.structure)genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);","((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"); species.structure<-matrix(0,5,5) diag(species.structure)<-1 name<-species.name(genetreevector[1]) sctree(genetreevector,name,name,species.structure)
This function can simulate a coalescence tree from a single population with parameter theta. The coalescence times in the tree have exponential distributions. theta is equal to 4uNe where Ne is the effective population size and u is the mutation rate.
sim.coaltree(nspecies,theta)sim.coaltree(nspecies,theta)
nspecies |
the number of species |
theta |
the population parameter |
theta is the population parameter theta=4N*mu.
The function returns the simulated coalescence tree.
Liang Liu [email protected]
John Wakeley, Coalescent theory: An introduction.
sim.coaltree(5,theta=0.2) ##[1] "((5:0.55696,(1:0.34858,3:0.34858):0.20838):2.99874,(2:0.97896,4:0.97896):2.57674)"sim.coaltree(5,theta=0.2) ##[1] "((5:0.55696,(1:0.34858,3:0.34858):0.20838):2.99874,(2:0.97896,4:0.97896):2.57674)"
The function simulates a gene tree from the species tree using Rannala and Yang's formula
sim.coaltree.sp(rootnode, nodematrix, nspecies, seq, name)sim.coaltree.sp(rootnode, nodematrix, nspecies, seq, name)
rootnode |
the root node of the species tree |
nodematrix |
the tree node matrix of the species tree |
nspecies |
the number of species |
seq |
a vector of number of sequences in each species |
name |
species names used in the simulated gene tree |
gt |
the gene tree generated from the species tree |
height |
the tree height of the gene tree |
Liang Liu [email protected]
Rannala, B. and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
tree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;" nodematrix<-read.tree.nodes(tree)$nodes rootnode<-7 spname<-species.name(tree) ##define the vector seq as [2,2,2,2] which means that there are 2 sequences in each species seq<-rep(2,4) str<-sim.coaltree.sp(rootnode,nodematrix,4,seq,name=spname)$gttree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;" nodematrix<-read.tree.nodes(tree)$nodes rootnode<-7 spname<-species.name(tree) ##define the vector seq as [2,2,2,2] which means that there are 2 sequences in each species seq<-rep(2,4) str<-sim.coaltree.sp(rootnode,nodematrix,4,seq,name=spname)$gt
The function generates a random gene tree from the species tree under the non-clock species tree model.
sim.coaltree.sp.mu(sptree, spname, seq, numgenetree,method="dirichlet",alpha=5.0)sim.coaltree.sp.mu(sptree, spname, seq, numgenetree,method="dirichlet",alpha=5.0)
sptree |
species tree |
spname |
species names |
seq |
the species-sequences struction, i.e., which sequence belongs to which species |
numgenetree |
the number of gene trees to be generated |
alpha |
the parameter in the gamma distribution. see also |
method |
either gamma or dirichlet |
gt |
the simulated gene tree |
st |
the node matrix of the species tree |
seqname |
the names of sequences |
Liang Liu
sptree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;" spname<-c("A","B","C","D") seq<-c(1,1,1,1) #each species has only one sequence. sim.coaltree.sp.mu(sptree, spname, seq, numgenetree=1,method="dirichlet",alpha=5.0)sptree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;" spname<-c("A","B","C","D") seq<-c(1,1,1,1) #each species has only one sequence. sim.coaltree.sp.mu(sptree, spname, seq, numgenetree=1,method="dirichlet",alpha=5.0)
Simulate DNA sequences from a tree using substitution model
sim.dna(nodematrix, seqlength, model, kappa=2, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4))sim.dna(nodematrix, seqlength, model, kappa=2, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4))
nodematrix |
the tree node matrix |
seqlength |
sequence length |
model |
1 JC, 2 H2P, 3 HKP, 4 GTR |
kappa |
the transition/transversion ratio |
rate |
the six rates used in GTR model |
frequency |
frequencies of four types of nucleotides |
The function returns DNA sequences simulated from the gene tree nodematrix. The sequences are coded as 1:A, 2:C, 3:G, 4:T.
Liang Liu [email protected]
Jukes, TH and Cantor, CR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
tree<-"(((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635);" nodematrix<-read.tree.nodes(tree)$nodes sim.dna(nodematrix,100, model=2, kappa=4)tree<-"(((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635);" nodematrix<-read.tree.nodes(tree)$nodes sim.dna(nodematrix,100, model=2, kappa=4)
The function simulates DNA sequences from a tree using the Jukes-Cantor model.
Liang Liu [email protected]
The function simulates sequences from a species tree.
simSeqfromSp(sptree, spname, ntaxasp, ngene, theta=0, noclock=0, simsequence=1, murate="Dirichlet",alpha=5, seqlength=100, model=1, kappa=2, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4), outfile, format="phylip")simSeqfromSp(sptree, spname, ntaxasp, ngene, theta=0, noclock=0, simsequence=1, murate="Dirichlet",alpha=5, seqlength=100, model=1, kappa=2, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4), outfile, format="phylip")
sptree |
A species tree which must be a rooted tree. |
spname |
species names |
ntaxasp |
a vector of the number of individuals in each species |
ngene |
number of genes |
theta |
population size |
noclock |
0: clocklike species tree 1: nonclocklike species tree |
simsequence |
1: simulate sequences and gene trees, 0: simulate gene trees |
murate |
distribution of mutation rates |
alpha |
the shape parameter of dirichlet distribution |
seqlength |
the number of nucleotides along the sequences |
model |
substitution model |
kappa |
transition/transversion ratio |
rate |
rates |
frequency |
nucleotide frequency |
outfile |
the full path of the output file |
format |
either "phylip" or "nexus" |
The function writes sequences into a file.
Liang Liu [email protected]
Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html
write.subtree, read.tree.string
#read the species tree from a data file data(sptree) outfile<-"out.txt" spname <- paste("S",1:20,sep="") outgroup <- "S20" ntaxasp <- rep(2,length(spname)) ntaxasp[length(spname)]<-1 ngene<-2 seqlength<-100 simSeqfromSp(sptree,spname,ntaxasp,noclock=1,ngene=ngene,seqlength=seqlength,model=1,outfile=outfile) simSeqfromSp(sptree,spname,ntaxasp,noclock=0,ngene=ngene,simsequence=0,seqlength=seqlength,model=1,outfile=outfile)#read the species tree from a data file data(sptree) outfile<-"out.txt" spname <- paste("S",1:20,sep="") outgroup <- "S20" ntaxasp <- rep(2,length(spname)) ntaxasp[length(spname)]<-1 ngene<-2 seqlength<-100 simSeqfromSp(sptree,spname,ntaxasp,noclock=1,ngene=ngene,seqlength=seqlength,model=1,outfile=outfile) simSeqfromSp(sptree,spname,ntaxasp,noclock=0,ngene=ngene,simsequence=0,seqlength=seqlength,model=1,outfile=outfile)
The function returns site patterns.
site.pattern(seq)site.pattern(seq)
seq |
DNA sequences with rows representing taxa and columns representing sites |
The function returns a matrix. Each row in the matrix represents a site pattern and the last number at each row is the frequency of the site pattern appeared in the DNA sequences.
Liang Liu [email protected]
seq<- matrix("A",nrow=4,ncol=5) seq[1,]<-c("A","A","G","C","C") seq[2,]<-c("A","G","G","C","C") seq[3,]<-c("T","A","G","C","C") seq[4,]<-c("A","A","G","T","T") site.pattern(seq)seq<- matrix("A",nrow=4,ncol=5) seq[1,]<-c("A","A","G","C","C") seq[2,]<-c("A","G","G","C","C") seq[3,]<-c("T","A","G","C","C") seq[4,]<-c("A","A","G","T","T") site.pattern(seq)
The function returns a sorted matrix
sortmat(mat, columns)sortmat(mat, columns)
mat |
a matrix |
columns |
the columns upon which the matrix is sorted |
The function returns a sorted matrix.
mat<-matrix(1:9,ncol=3) sortmat(mat,1)mat<-matrix(1:9,ncol=3) sortmat(mat,1)
The function can be used to obtain species names from a tree string.
species.name(str)species.name(str)
str |
a tree string in the parenthetical format |
The function returns the species names. If the tree string contains only the node number instead of species names, the function will return the node numbers.
The function returns the species names.
Liang Liu [email protected]
tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" species.name(tree.string)tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" species.name(tree.string)
This function can create a matrix to present the sequence-species relationship.
spstructure(numsgenenodes)spstructure(numsgenenodes)
numsgenenodes |
number of sequences for each species |
The matrix created by this function can be used as species.structure.
Liang Liu
numsgenenodes<-c(1,1,1,1,1,2,2,1,1,1,1,2,3,2,2,2,1,1,1,2,1,8,2,2,2,1,1,1) species.structure<-spstructure(numsgenenodes)numsgenenodes<-c(1,1,1,1,1,2,2,1,1,1,1,2,3,2,2,2,1,1,1,2,1,8,2,2,2,1,1,1) species.structure<-spstructure(numsgenenodes)
a species trees
data(sptree)data(sptree)
Liang Liu [email protected]
data(sptree) read.tree.nodes(sptree)data(sptree) read.tree.nodes(sptree)
The function can build a STAR tree from a set of gene trees.
star.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj")star.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj")
trees |
the gene tree vector |
speciesname |
species names |
taxaname |
taxa names |
species.structure |
a matrix defining the species-taxa relationship |
outgroup |
outgroup |
method |
UPGMA or NJ |
The function returns a STAR tree.
Liang Liu [email protected]
#create three gene trees treestr<-rep("",4) treestr[1]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[2]<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[3]<-"((((O:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,H:0.01635):0.1,W:0.11635);" treestr[4]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" speciesname<-species.name(treestr[1]) taxaname<-speciesname species.structure<-matrix(0,ncol=5,nrow=5) diag(species.structure)<-1 star.sptree(treestr, speciesname, taxaname, species.structure,outgroup="W",method="nj")#create three gene trees treestr<-rep("",4) treestr[1]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[2]<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[3]<-"((((O:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,H:0.01635):0.1,W:0.11635);" treestr[4]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" speciesname<-species.name(treestr[1]) taxaname<-speciesname species.structure<-matrix(0,ncol=5,nrow=5) diag(species.structure)<-1 star.sptree(treestr, speciesname, taxaname, species.structure,outgroup="W",method="nj")
The function can build a STEAC tree from a set of gene trees.
steac.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj")steac.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj")
trees |
the gene tree vector |
speciesname |
species names |
taxaname |
taxa names |
species.structure |
a matrix defining the species-taxa relationship |
outgroup |
outgroup |
method |
UPGMA or NJ |
The function returns a STEAC tree.
Liang Liu [email protected]
#create three gene trees treestr<-rep("",4) treestr[1]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[2]<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[3]<-"((((O:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,H:0.01635):0.1,W:0.11635);" treestr[4]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" speciesname<-species.name(treestr[1]) taxaname<-speciesname species.structure<-matrix(0,ncol=5,nrow=5) diag(species.structure)<-1 steac.sptree(treestr, speciesname, taxaname, species.structure,outgroup="W",method="nj")#create three gene trees treestr<-rep("",4) treestr[1]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[2]<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr[3]<-"((((O:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,H:0.01635):0.1,W:0.11635);" treestr[4]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" speciesname<-species.name(treestr[1]) taxaname<-speciesname species.structure<-matrix(0,ncol=5,nrow=5) diag(species.structure)<-1 steac.sptree(treestr, speciesname, taxaname, species.structure,outgroup="W",method="nj")
The function returns the subtree under the node inode
subtree(inode, name, nodematrix)subtree(inode, name, nodematrix)
inode |
the root node of the subtree |
name |
the species names |
nodematrix |
the tree node matrix |
The function returns the tree string of the subtree.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names subtree(7,spname,nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names subtree(7,spname,nodematrix)
calculate the total branch length of a sub-tree under inode.
subtree.length(inode, nodes, nspecies)subtree.length(inode, nodes, nspecies)
inode |
the root node of the sub-tree |
nodes |
the tree node matrix |
nspecies |
the number of species in the tree |
The node matrix is the output of the function read.unrooted.nodes or read.rooted.nodes. The function can calculate the total branch length of a tree if inode is set to be the root node. If inode is not the root node, subtree.length calculates the total branch length of a sub-tree.
The function returns the total branch length of a sub-tree.
Liang Liu [email protected]
tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" nodes<-read.tree.nodes(tree.string)$nodes subtree.length(6,nodes,4)tree.string<-"(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);" nodes<-read.tree.nodes(tree.string)$nodes subtree.length(6,nodes,4)
The function swapps two subtrees.
swap.nodes(inode, jnode, name, nodematrix)swap.nodes(inode, jnode, name, nodematrix)
inode |
the root node of the first subtree |
jnode |
the root node of the second subtree |
name |
the species names |
nodematrix |
the tree node matrix |
nodes |
the tree node matrix after swapping |
treestr |
the tree string after swapping |
The function is unable to swap two overlapped subtrees.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names swap.nodes(1,2,spname,nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names swap.nodes(1,2,spname,nodematrix)
This function calculates the distance between two trees.
treedist(tree1,tree2)treedist(tree1,tree2)
tree1 |
the first tree node matrix |
tree2 |
the second tree node matrix |
The function returns the distance of two trees.
Liang Liu [email protected]
treestr1<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr2<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" name<-species.name(treestr1) nodematrix1<-read.tree.nodes(treestr1,name)$nodes nodematrix2<-read.tree.nodes(treestr2,name)$nodes treedist(nodematrix1,nodematrix2)treestr1<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" treestr2<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);" name<-species.name(treestr1) nodematrix1<-read.tree.nodes(treestr1,name)$nodes nodematrix2<-read.tree.nodes(treestr2,name)$nodes treedist(nodematrix1,nodematrix2)
The function calculates the loglikelihood for DNA sequences (snip data)
tripleloglike(sptree,spname,dna)tripleloglike(sptree,spname,dna)
sptree |
species tree |
spname |
species names |
dna |
dna sequences |
This function is used to calculate the loglikelihood of triples.
The function returns the loglikehood of triples.
Liang Liu [email protected]
write.subtree, read.tree.string
This is an internal function used to calculate the loglikelihood of triples.
triplenumber(dna)triplenumber(dna)
dna |
DNA sequences |
This function is used to calculate triple likelihoods.
The function returns the number of triples.
Liang Liu [email protected]
write.subtree, read.tree.string
This is an internal function used to calculate the loglikelihood of triples.
triplepara(inode,jnode,nodematrix,nspecies)triplepara(inode,jnode,nodematrix,nspecies)
inode |
the decendant node in the triple |
jnode |
the ancestral node in the triple |
nodematrix |
the species tree |
nspecies |
the number of species |
This function is used to calculate triple likelihoods.
The function returns the theta and gamma in a triple.
Liang Liu [email protected]
write.subtree, read.tree.string
The function calculates the probability of a set of rooted triples.
tripleProb(para)tripleProb(para)
para |
theta and gamma |
Liang Liu [email protected]
An example of unrooted trees
data(unrooted.tree)data(unrooted.tree)
Liang Liu [email protected]
data(unrooted.tree) read.tree.nodes(unrooted.tree[1])data(unrooted.tree) read.tree.nodes(unrooted.tree[1])
unroot a tree.
unroottree(nodematrix)unroottree(nodematrix)
nodematrix |
the tree node matrix |
The function returns an unrooted tree.
Liang Liu [email protected]
treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names unroottree(nodematrix)treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);" nodematrix<-read.tree.nodes(treestr)$nodes spname<-read.tree.nodes(treestr)$names unroottree(nodematrix)
The function computes the UPGMA tree from multiple gene trees.
upgma(dist, name, method="average")upgma(dist, name, method="average")
dist |
a distance matrix |
name |
the species names |
method |
the method for recalculate pairwise distances. two options: averge or min. |
The function returns a tree node matrix, a tree string and species names.
Liang Liu [email protected]
dist<-matrix(runif(25),5,5) dist<-(dist+t(dist))/2 diag(dist)<-0 upgma(dist,name=c("H","G","C","O","W"))dist<-matrix(runif(25),5,5) dist<-(dist+t(dist))/2 diag(dist)<-0 upgma(dist,name=c("H","G","C","O","W"))
write sequences to a Nexus file.
write.dna(sequence, name, file = "", format="nexus", program="mrbayes",partition=matrix(0,ncol=2,nrow=1), clock=0, popmupr=0, ngen=1000000,nrun=1,nchain=1,samplefreq=100,taxa=as.vector,burnin=1000,gamma="(3,0.02)", outgroup=1,outfile="",append = FALSE)write.dna(sequence, name, file = "", format="nexus", program="mrbayes",partition=matrix(0,ncol=2,nrow=1), clock=0, popmupr=0, ngen=1000000,nrun=1,nchain=1,samplefreq=100,taxa=as.vector,burnin=1000,gamma="(3,0.02)", outgroup=1,outfile="",append = FALSE)
sequence |
DNA sequences |
name |
taxa names |
file |
output file |
program |
either mrbayes or best. |
format |
nexus or phylip |
partition |
each partition corresponds a gene or a locus. |
clock |
1:clock, 0:no clock |
popmupr |
for non-clock species tree model |
ngen |
number of generations |
nrun |
number of runs |
nchain |
number of chains |
samplefreq |
sampling frequency |
taxa |
species names if best is defined |
burnin |
burn in |
outgroup |
the node number of the outgroup |
outfile |
output file |
append |
append or not |
gamma |
parameters in the inverse gamma distribution as the prior of theta. |
Liang Liu
write a tree or a sub-tree into a string in parenthetical format
write.subtree(inode, nodes, nspecies,inodeindex)write.subtree(inode, nodes, nspecies,inodeindex)
inode |
the root node of a sub-tree |
nodes |
a tree node matrix |
nspecies |
the number of species |
inodeindex |
the root node of a sub-tree |
If inode is the root of the tree, the function will write the whole tree into a string in parenthetical format. If inode is not the root node, the function will write the sub-tree into a string. The function works for both rooted trees and unrooted trees.
The function returns a tree string in parenthetical format
Liang Liu [email protected]
write.tree.string, read.tree.nodes
data(rooted.tree) tree<-read.tree.nodes(rooted.tree[1]) tree$nodes tree$names write.subtree(7,tree$nodes,length(tree$names),7)data(rooted.tree) tree<-read.tree.nodes(rooted.tree[1]) tree$nodes tree$names write.subtree(7,tree$nodes,length(tree$names),7)
The function writes tree strings to a file in NEXUS or PHYLIP format.
write.tree.string(X, format = "Nexus", file = "", name = "")write.tree.string(X, format = "Nexus", file = "", name = "")
X |
a vector of tree strings |
format |
tree file format |
file |
the file name |
name |
the species names |
If name is provided, the function will use name as the species names in the translation block in the NEXUS tree file. Otherwise, the species names will be extracted from the tree strings.
The function returns a tree file in the format of NEXUS or PHYLIP.
Liang Liu [email protected]
Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html
write.subtree, read.tree.string