Evolutionary model can be chosen with -model option.
- jc
- k2p : parameter kappa can be set with -parameters
- f81 : parameters can be set with -parameters <piA,piC,piG,piT>
- gtr : parameters can be set with -parameters <d,f,b,e,a,c,piA,piC,piG,piT>, with gtr matrix being: ⌈ * d f b ⌉ | d * e a | | f e * c | ⌊ b a c * ⌋
- jtt (https://doi.org/10.1093/bioinformatics/8.3.275)
- wag (https://doi.org/10.1093/oxfordjournals.molbev.a003851)
- lg (https://doi.org/10.1093/molbev/msn067)
- hivb (https://doi.org/10.1371/journal.pone.0000503)
- ab (https://doi.org/10.1093/molbev/msu340)
- mtrev (https://doi.org/10.1007/bf02498640)
By default, site rates follow a discrete gamma distribution with a shape parameter (alpha) of 1.0 and 4 categories, but it is possible to :
- disable the gamma distribution with: -gamma=false
- use a continuous gamma distribution with: -discrete=false
- change the number of categories with: -gamma-cat=6
- change the alpha parameter with: -alpha=0.8
- provide an input file with site rates, with
-rates <file>. In this case, other rate related options are ignored (-gamma,-gamma-cat,-alpha,-discrete), and site rates are taken from the file. There must be exactly one rate per site. Otherwise, the other options are taken into account.
Usage of ./snag:
-alpha float
gamma shape parameter (default 1)
-ancestral
If true, then write ancestral sequences as internal nodes comments in the output tree file
-discrete
discrete gamma distribution (default true)
-gamma
enable gamma distribution of site rates (default true)
-gamma-cat int
number of gamma categories (default 4)
-help
help
-intree string
Input tree (default "stdin")
-length int
Simulated alignment length (default 100)
-model string
Evolutionary model (for dna: jc, k2p, f81, gtr; for aa: jtt, wag, lg, hivb, mtrev, ab) (default "k2p")
-num-aligns int
number of alignments to simulate per input tree (default 1)
-out-align string
Output alignment file (default "stdout")
-out-rates string
Output site rates file (default "stdout")
-out-trees string
Output tree file with real nb mutations as branch lengths and potentially ancestral sequences at internal nodes (default "stdout")
-parameters string
Model parameters: k2p: 'kappa'; f81: 'piA,piC,piG,piT'; gtr: 'd,f,b,e,a,c,piA,piC,piG,piT, amino-acid models: piA, piR, piN, piD, piC, piQ, piE, piG, piH, piI, piL, piK, piM, piF, piP, piS, piT, piW, piY, piV (otherwise: take model frequencies)'
-rates string
Input site rate file (one rate per line), if given, -gamma, -alpha, -discrete and -gamma-cat are ignored (default "none")
-root-seq string
Fasta file with sequence to take as root (invalidates -length)
-seed int
Random Seed parameter (default 1699004613724063000)
-version
Display version of snag