HoT: Heads or Tails Alignment Reliability
In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

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

MSA reliability assessment HoT (Landan and Graur 2008)

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HoT(sequences, method = "auto", bootstrap, n.coopt = "auto",
  plot_guide = TRUE, store_msas = FALSE,
  msa.exec = "/usr/local/bin/mafft", ncore = 1, zip.file)

`sequences`	object of class `DNAbin` or `AAbin` containing unaligned sequences of DNA or amino acids.
`method`	further argument passed to MAFFT, default is `"auto"`
`bootstrap`	integer giving the number of alternative MSAs to be computed
`n.coopt`	Character string, xxx.
`plot_guide`	Logical, xxx.
`store_msas`	Logical, xxx.
`msa.exec`	character string giving the path to the executable of the alignment program (e.g. "/usr/local/bin/mafft"); Must be on of: 'mafft', 'muscle', 'clustalo', 'clustalw2'
`ncore`	integer specifying the number of cores; default = 1 (serial), "auto" can be used for automated usage of all detected cores.
`zip.file`	A character string giving the name for the output zip file.

Calculates column reliability (and other scors) by comparing alternative MSAs generated by aligning guide tree partitions as described in Landan and Graur (2008). For details see compareMSAs. 8*(N-3) alternative MSAs are generated by default, where N is the number of sequences.

object of class polenta: msa original MSA as computed by msa.program scores residue pair score

Franz-Sebastian Krah

G. Landan and D. Graur. 2008. Local reliability measures from sets of co-optimal multiple sequencesuence alignments. 13:15–24

msa_set_scoreR, guidance, guidance2

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