Description Usage Arguments Value Author(s) See Also
Filtering of the base MSA using polenta scores
1 2 3 |
polenta |
object of class |
col.cutoff |
numeric between 0 and 1; removes unreliable columns below the cutoff (default: 0.2); ignored if FALSE |
seq.cutoff |
numeric between 0 and 1; removes unreliable sequences below the cutoff (default: 0.1); ignored if FALSE |
mask.cutoff |
residues below the cutoff are masked ('N' for DNA, 'X' for AA; default: 0.5); ignored if FALSE |
filter.ends |
logical, if TRUE trim.ends (ips) is applied to the MSA |
filter.gaps |
logical, if TRUE trim.gabs (ips) is applied to the MSA |
column_score |
logical, if TRUE column score (e.g. for RAxML: flag -a) is in the output |
flag_a |
character specifying a path. If path is supplied function writes the filtered MSA into a fasta file. Additionally the function produces a file with the column score ready for RAxML input (flag -a) |
na.coding |
XXX. |
masked MSA of class AAbin
or DNAbin
column_score is optional
Franz-Sebastian Krah
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