guidance2: MSA Reliability Assessment with GUIDANCE2
In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description Usage Arguments Details Value Author(s) References See Also

Calculate MSA reliability scores with GUIDANCE2 (Sela et al. 2015).

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guidance2(sequences, bootstrap = 100, method = "auto", n.coopt = 4,
  n.part = "auto", msa.exec = "/usr/local/bin/mafft", ncore = 1,
  store_msas = FALSE, zip.file)

`sequences`	An object of class `DNAbin` or `AAbin` containing unaligned sequences of DNA or amino acids.
`bootstrap`	An integer giving the number of alternative MSAs to be computed.
`method`	A character string containing further arguments passed to MAFFT; default is `"auto"`.
`n.coopt`	An integer giving the number of sampled co-optimal MSAa.
`n.part`	XXX.
`msa.exec`	A character string giving the path to the executable of the alignment program (e.g. `/usr/local/bin/mafft`); possible programs are `MAFFT`, `MUSCLE`, `ClustalO`, and `ClustalW`.
`ncore`	An integer specifying the number of cores; default = 1 (i.e. serial execution); `"auto"` can be used for automated usage of all detected cores.
`zip.file`	A character string giving the name of zip-compressed file, which contains the alternative MSAs. If left empty (default), the alternative MSA will not be stored and cannot be assessed by the user.

Calculates column confidence (and other scors) by comparing alternative MSAs generated by the GUIDANCE with varying gap opening panelty and the HoT methodology. First 100 alternative MSAs (with BP guide trees) with varying gap opening panelty are produced, then for each n (default = 4) co-optimal alignments are produced using HoT. The basic comparison between the BP MSAs and a reference MSA is if column residue pairs are identically aligned in all alternative MSAs compared with the base MSA (see compareMSAs).

An object of class polentaDNA or polentaAA.

Franz-Sebastian Krah

Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.

Landan, G. and D. Graur. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pacific Symposium on Biocomputing 13:15–24.

Penn, O., E. Privman, G. Landan, D. Graur, and T. Pupko. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.

Sela et al. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research 43:W7–W14

guidance, HoT

heibl/polenta documentation built on May 17, 2019, 3:22 p.m.