Parameters

`pairs = 1`: Method for generating the list of sequence pairs to use: 2 use phylogenetic tree built with`ednapars`(maximum parsimony); 1 use phylogenetic tree built with`ednaml`(maximum likelihood); 0 or other use user-input file.*prefix*.pairs`refpos = 0`: 0 use seperate CDS files for each sequence; 1 or other use reference sequence CDS files for all sequences.`gbkpos = 0`: 0 get CDS files from(or*seqname*.fasta.orfs) files; 1 or other get CDS files from*seqname*.gbk.orfsfiles (for any*seqname*.gbkfiles, the*seqname*.fastafile, if any, will be used).*seqname*.fasta.orfs`skip = 0`: 1 or other skip sequence files containing non-ACGTUacgtu characters (exits if the reference sequence contains non-ACGTUacgtu characters); 0 read standard ambiguous nt codes as N and ignore for most statistics (ambiguous nt are logged along with the gaps; codons containing ambiguous nt are logged along with the `zero-probability' transitions).`window1 = 5`: , where the running mean sliding window size for the 1st, 2nd and 3rd codon positions and for the 4-fold degenerate neutral sites plots is nt (or codons).`window2 = 10`: , where the running mean sliding window size for the all sites and for the non-coding sites plots is nt.`circular = 1`: 0 not a circular genome; 1 or other circular genome.`clip1 = 0.00`: Upper clipping threshold for clipped running mean:`clip1 = 0.05`means that the upper 5% (i.e. columns with low observed number of mutations relative to expected number of mutations) in each window are clipped before calculating the mean.`clip2 = 0.30`: Lower clipping threshold for clipped running mean:`clip2 = 0.05`means that the lower 5% (i.e. the columns with high observed number of mutations relative to expected number of mutations) in each window are clipped before calculating the mean.`tttmin = 0.0`: Lowest value to use in -fitting.`tttmax = 10.0`: Highest value to use in -fitting.`tVfit = 0.2`: Required fitting accuracy (total number of mutations between a sequence pair) for and .`maxiter = 20`: Maximum number of fitting iterations for and .`Vmin = 0.01`: Lowest value to use in -fitting ( 0.01).`Vmax = 10.0`: Highest value to use in -fitting ( 10).`Vtype = 1`: 0 find seperate value for each sequence pair; 1 or other find one value for the alignment.`Vfix = 0`: If 0, use this value for all sequence pairs (defaults to 1 if 0; overridden if`fitwhat = 3`).`fitwhat = 3`: 0 or other fit using total number of mutations; 1 fit using number of neutral/synonymous mutations; 2 fit using number of neutral/synonymous mutations at 4-fold degenerate sites; 3 as for 2, then adjust to fit the total number of mutations (i.e. including nonsynonymous mutations). Note: 1--3 are not recommended if the sequence is predominantly double-coding since, in this case, the number of neutral sites is potentially very small.`wholeseq = 1`: Nucleotide range to use for all model-fitting, statistics and plots: 0 use the region`range1`--`range2`, 1 or other use the whole sequence.`range1 = 0`: Start nucleotide of region to analyse (if`wholeseq = 0`; otherwise ignored), in reference sequence coordinates.`range2 = 0`: End nucleotide of region to analyse (if`wholeseq = 0`; otherwise ignored), in reference sequence coordinates.