HoT: Heads or Tails alignment reliability

In heibl/rpg: Multiple Sequence Alignment with PASTA and GUIDANCE

Description

MSA reliability assessment HoT (Landan and Graur 2008)

Usage

HoT(sequences, msa.program = "mafft", exec, type, n.coopt = "auto",
  col.cutoff = "auto", seq.cutoff = "auto", mask.cutoff = "auto",
  parallel = FALSE, ncore = "auto", method = "auto", plot_guide = TRUE,
  alt.msas.file)

Arguments

sequences	An object of class DNAbin or AAbin containing unaligned sequences of DNA or amino acids. @param cutoff specifies a cutoff to remove unreliable columns below the cutoff
msa.program	A charcter string giving the name of the MSA program, one of c("mafft", "muscle", "clustalo", "clustalw2"); MAFFT is default
exec	A character string giving the path to the executable of the alignment program.
col.cutoff	numberic between 0 and 1; specifies a cutoff to remove unreliable columns below the cutoff; either user supplied or "auto" (0.73)
seq.cutoff	numberic between 0 and 1; specifies a cutoff to remove unreliable sequences below the cutoff; either user supplied of "auto" (0.5)
mask.cutoff	specific residues below a certain cutoff are masked ('N' for DNA, 'X' for AA); either user supplied of "auto" (0.5)
parallel	logical, if TRUE, specify the number of cores
ncore	number of cores (default is 'auto')
method	further arguments passed to MAFFT, default is "auto"

Details

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.

Value

list containing following scores and alignments:

mean_scores residue pair score and mean column score

column_score

residue_column_score column reliability

residue_pair_residue_score

residual_pair_sequence_pair_score

residual_pair_sequence_score

residue_pair_score

base_msa

HoT_msa is the base_MSA removed from unreliable residues/columns/sequences below cutoffs

Author(s)

Franz-Sebastian Krah

Christoph Heibl

References

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

See Also

compareMSAs, guidance, guidance2

heibl/rpg documentation built on May 17, 2019, 3:23 p.m.