paraFixSites(x, ...) # S3 method for phylo paraFixSites( x, alignment = NULL, seqType = c("AA", "DNA", "RNA"), Nmin = NULL, reference = NULL, gapChar = "-", minSkipSize = NULL, ... ) # S3 method for treedata paraFixSites(x, ...) # S3 method for lineagePath paraFixSites( x, minEffectiveSize = NULL, searchDepth = 1, method = c("compare", "insert", "delete"), ... ) # S3 method for sitesMinEntropy paraFixSites( x, category = c("intersect", "union", "parallelOnly", "fixationOnly"), minSNP = NULL, mutMode = c("all", "exact", "pre", "post"), ... )
lineagePath object returned from
further arguments passed to or from other methods.
alignment object. This commonly can be from
sequence parsing function in the
seqinr package. Sequence
names in the alignment should include all
tip.label in the tree
The type of the sequence in the alignment file. The default is "AA" for amino acid. The other options are "DNA" and "RNA".
The parameter for identifying phylogenetic pathway using SNP. If
provided as fraction between 0 and 1, then the minimum number of SNP will
be total tips times
Nmin. If provided as integer greater than 1, the
minimum number will be
Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering
The character to indicate gap. The numbering will skip the
gapChar for the reference sequence.
The minimum number of tips to have gap or ambiguous amino acid/nucleotide for a site to be ignored in other analysis. This will not affect the numbering. The default is 0.8.
The minimum number of tips in a group.
The function uses heuristic search but the termination of
the search cannot be intrinsically decided.
searchDepth is needed to
tell the search when to stop.
The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.
The minimum number of mutations to be qualified as parallel on at least two lineages. The default is 1.
The strategy for finding parallel site. The default
is to consider any mutation regardless of the amino acid/nucleotide before
and after mutation; Or
exact to force mutation to be the same; Or
post to select the site having amino acid/nucleotide