raxmlBackbone: RAxML phylogeny with backbone tree.
In fkeck/diatobc: Bioinformatic toolbox for my projects

Description Usage Arguments Details Value References See Also

This function uses RAxML to reconstruct a tree given an alignment and a backbone tree (the -g option of RAxML).

1 2	raxmlBackbone(x, backbone, model, raxml.exec, nruns = 1, bs = NULL, part = NULL, threads = NULL, MLSCC = FALSE, quiet = FALSE)

`x`	an alignment of sequences of class `DNAbin`.
`backbone`	a phylogenetic tree (class `phylo`) to use as a constraint. The tip labels must match with the appropriate DNA sequences labels. Use `NULL` for no constraint.
`model`	a character string giving the substitution model to use (the -m option of RAxML).
`raxml.exec`	a character string giving the path of the program.
`nruns`	the number of independent ML searches (runs). This is ignored if bootstrapping is enabled. Then the number of ML searches will be the number of bootstraps set with `bs` divided by 5.
`bs`	a numeric giving the number of rapid bootstraps to perform.
`part`	a vector of integers giving the boundaries of the different partitions, if relevant. E.g. `c(1, 5355, 5356, 7633)` for a two genes partition.
`threads`	the number of threads to use, if available.
`MLSCC`	a logical indicating whether to use the ML search convergence criterion (the -D option of RAxML). This is a shortcut in ML search which can improve significantly the speed for large phylogenies.
`quiet`	a logical indicating whether RAxML warnings are printed on console (available only for RAxML v8+).

Since RAxML doesn't support special characters in taxa/sequence names, they are deleted automatically with a warning. Be warned that deletion of illegal characters may lead to ambiguities in taxa/sequence names.

A list of two elements: