[アミノ酸の rate matrix を選択]

model = 3
* models for codons:
* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
* models for AAs or codon-translated AAs:
* 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

[データセットで観察されるアミノ酸組成を進化モデルに反映させます．F オプションと呼ばれています]

NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
* 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
* 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
* 13:3normal>0

icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
Mgene = 2
* codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
* AA: 0:rates, 1:separate

[partition ごとにアミノ酸組成 (pi: パイ) を算出します]

* ndata = 10
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 2 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = .4 * initial or fixed omega, for codons or codon-based AAs

fix_alpha = 0 * 0: estimate gamma shape parameter; 1: fix it at alpha

[gamma shape パラメーターを推定させます]

alpha = 0.3 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 1 * 1:different alphas for genes

[partition (ここでは gene としています) ごとに alpha を推定させます]

ncatG = 5 * # of categories in dG of NSsites models

[gamma のカテゴリー数]

getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

Small_Diff = .5e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time


* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.