max_likelihood: function to calculate a maximum likelihood phylogenetic tree
In geantonicelli/firstPackage: set of wrapper functions for phylogenetic analysis

Description Usage Arguments Value Author(s) See Also Examples

this function is a wrapper around the functions 'dist.alignment', 'dist.dna', 'nj', 'bionj', 'fastme.bal', 'fastme.ols', 'pml' and 'optim.pml'. it takes a sequences alignment in format 'alignment' of 'DNAbin' matrix and perform all transformations and steps to calculate a phylogenetic distance matrix based on similarity or identity in the case of proteins or based in evolutionary models in the case of DNA or RNA, to perform a likelihood-based phylogenetic clustering and to optimise the phylogeny by a maximum likelihood algorithm

max_likelihood(
  alignment,
  type,
  model = TN93,
  clustering = bionj,
  pml.model = NULL,
  outgroup = NULL,
  clean = TRUE
)

`alignment`	an object of class alignment or DNAbin containing a DNA, RNA or protein sequences alignment
`type`	a character string without ” specifying the type of sequences, i.e. DNA, RNA or protein (without default value)
`model`	a character string without ” specifying the model to be used for the calculation of the distances matrix, i.e. raw, N, TS, TV, JC69, K80, F81, K81, F84, BH87, T92, TN93 (default), GG95, logdet, paralin, indel, or indelblock
`clustering`	a character string without ” specifying the clustering algorithm to be used to build the phylogenetic tree, i.e classic neighbor-joining (nj), improved neighbor-joining (bionj) (default), NJ or bio-NJ from a distance matrix with possibly missing values (njs, bionjs), balanced minimum evolution principle (fastme.bal), ordinary least-squares minimum evolution principle (fastme.ols)
`pml.model`	a character string without ” specifying the model to be used for the calculation and optimisation of the maximum likelihood, for nucleotide sequences they are 23, i.e. JC, F81, K80, HKY, TrNe, TrN, TPM1, K81, TPM1u, TPM2, TPM2u, TPM3, TPM3u, TIM1e, TIM1, TIM2e, TIM2, TIM3e, TIM3, TVMe, TVM, SYM, GTR, whereas for protein sequences there are 17 algorithms available, i.e. WAG, JTT, LG, Dayhoff, cpREV, mtmam, mtArt, MtZoa, mtREV24, VT, RtREV, HIVw, HIVb, FLU, Blosum62, Dayhoff_DCMut, JTT_DCMut. The default model corresponds to the model F81 for nucleotides and it is set up with the parameters 'optBf=TRUE' and 'optQ=FALSE' in the function 'optim.pml()' of the phangorn package inside the function 'max_likelihood()'. It is possible to run all the models at once for a given type of sequence with the value 'all' without ”
`outgroup`	a character string without ” specifying a taxon to be taken as root for building the tree. The default value is NULL leading to an unrooted tree
`clean`	logical (default=TRUE) indicating if the input sequences should be cleaned of any gap position or undefined nucleotide or aminoacid residue to improve philogenetic prediction, set to FALSE if you want to clean the sequences more gently and flexibly with 'clean_alignment' before calculations or if you want to use the raw sequences alignment

the function returns an object of class 'pml' of the 'phangorn' package. Advanced and elaborated plots can be drawn in later steps based on the tree data of the pml class object

gerardo esteban antonicelli

'retrieve_seqs' 'print_alignment' 'clean_alignment' 'load_alignment' 'make_tree' 'max_parsimony'

data(fastaRNA)
data(phylipProt)
mytree <- max_likelihood(fastaRNA, type=RNA, clustering=fastme.bal,
                        pml.model=GTR, clean=FALSE)
## Not run: mytree <- max_likelihood(phylipProt, type=protein, pml.model=Blosum62,
                        outgroup=YP_0010399)
## End(Not run)
## Not run: plot.phylo(mytree, type='u')