R: Phylogenetic Analysis by Maximum Likelihood for Nucleotide...

paml.baseml {phyclust} | R Documentation

## Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences

### Description

This function modifies the original standalone code of `baseml` in PAML developed by Yang (1997) for phylogenetic analysis by maximum likelihood. This function provides a way to generate an ancestral tree for given central sequences clustered by `phyclust`.

### Usage

    paml.baseml(X, seqname = NULL, opts = NULL, newick.trees = NULL)
    paml.baseml.control(...)
    paml.baseml.show.default()

### Arguments

`X` | nid matrix with N rows/sequences and L columns/sites.
`seqname` | sequence names.
`opts` | options as the standalone version, provided by `paml.baseml.contol`.
`newick.trees` | a vector/list contains NEWICK trees for `runmode = 2`.
`...` | for other possible opts and values. See PAML manual for details.
`show` | show opts and values.

### Details

The function `paml.baseml` directly reuses the C code of `baseml` of PAML, and the function `paml.baseml.control` is to generate controls for `paml.baseml` as the file `baseml.ctl` of PAML.

The `seqname` should be consistent with `X`, and the leaf nodes of `newick.trees`.

The options `opts` is followed from the original `baseml.ctl` except `seqfile`, `treefile` and `outputfile` will be omitted.

`paml.baseml.control` generates default `opts`, and `paml.baseml.show.default` displays annotations for the default `opts`.

### Value

This function returns a list, and each element stores one line of outputs of `baseml` separated by newline. The list stores in a class `baseml`. All the output of `baseml` of PAML will be saved in several files, and these will be read in by `scan`. Further post processing can be done by parsing the returning vector. The details of output format can found on the website http://abacus.gene.ucl.ac.uk/software/paml.html and its manual.

Note that some functionalities of `baseml` of PAML are changed in `paml.baseml` due to the complexity of input and output. The changes include such as disable the option `G` and rename the file `2base.t` to `pairbase.t`.

Typically, the list contains the original output of `baseml` including `pairbase.t`, `mlb`, `rst`, `rst1`, and `rub` if they are not empty. The best tree (unrooted by default) will be stored in `best.tree` parsed from `mlb` based on the highest log likelihood. All output to `STDOUT` are stored in `stdout`. No `STDIN` are allowed.

Note that the print function for the class `baseml` will only show the `best.tree` only. Use `str` or `names` to see the whole returns of the list.

### Warning(s)

Carefully read the PAML's original document before using the `paml.baseml` function, and `paml.baseml` may not be ported well from `baseml` of PAML. Please double check with the standalone version.

`baseml` may not be a well designed program, and may run slowly. If it were stuck, temporary files would all store at a directory obtained by `tempfile("/paml.baseml.")`.

`baseml` has its own options and settings which may be different than phyclust and ape. For example, the following is from the PAML's document, “In PAML, a rooted tree has a bifurcation at the root, while an unrooted tree has a trifurcation or multifurcation at the root.” i.e. `paml.baseml` uses a rooted result for an unrooted tree, as well as for a rooted tree.

`baseml` also needs a sequence file which is dumped from R (duplicated from memory) for `paml.baseml`, and this file can be very big if sequences are too long or number of sequences is too large. Also, `paml.baseml` may take long time to search the best tree if data are large or initial trees are not provided.

### Author(s)

Yang, Z. (1997) and Yang, Z. (2007)

Maintain: Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

Yang, Z. (1997) “PAML: a program package for phylogenetic analysis by maximum likelihood”, Computer Applications in BioSciences, 13, 555-556.

Yang, Z. (2007) “PAML 4: a program package for phylogenetic analysis by maximum likelihood”, Molecular Biology and Evolution, 24, 1586-1591. http://abacus.gene.ucl.ac.uk/software/paml.html

### See Also

`print.baseml`, `write.paml`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    paml.baseml.show.default()

    ### Generate data.
    set.seed(123)
    ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
    ret.seqgen <- seqgen(opts = "-mHKY -l40 -s0.2", newick.tree = ret.ms[3])
    (ret.nucleotide <- read.seqgen(ret.seqgen))
    X <- ret.nucleotide$org
    seqname <- ret.nucleotide$seqname

    ### Run baseml.
    opts <- paml.baseml.control(model = 4, clock = 1)
    (ret.baseml <- paml.baseml(X, seqname = seqname, opts = opts))
    (ret.baseml.init <- paml.baseml(X, seqname = seqname, opts = opts,
       newick.trees = ret.ms[3]))
    ret.ms[3]

    ### Unrooted tree.
    opts <- paml.baseml.control(model = 4)
    (ret.baseml.unrooted <- paml.baseml(X, seqname = seqname, opts = opts))

    ### More information.
    opts <- paml.baseml.control(noisy = 3, verbose = 1, model = 4, clock = 1)
    ret.more <- paml.baseml(X, seqname = seqname, opts = opts)
    # ret.more$stdout

    ### Plot trees
    par(mfrow = c(2, 2))
    plot(read.tree(text = ret.ms[3]), main = "true")
    plot(read.tree(text = ret.baseml$best.tree), main = "baseml")
    plot(read.tree(text = ret.baseml.init$best.tree), main = "baseml with initial")
    plot(unroot(read.tree(text = ret.baseml.unrooted$best.tree)),
         main = "baseml unrooted")

    ## End(Not run)

[Package phyclust version 0.1-30 Index]