检查你的输入文件格式和视频里面是否一致,仔细看看课
程序运行中无报错,但是输出的figtree里面分化时间是NAN。如下:UTREE 1 = (((Spermwhale: -nan, (Cow: -nan, Sheep: -nan)。我用seq模式和近似自然法都是同样的情况,我的序列是cds序列,我输入的树文件是:(((A,(C,S)'U(0.15)')'B(0.47,0.58)',((((B,LA),BK),DR),(H,W))),Ho)'B(0.728,0.783)';我的控制文件如下,请问是哪里出了问题:
seed = -1
seqfile = single_copy.cds_msa_trimed.phy
treefile = input.tree
outfile = out
ndata = 1
seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
usedata = 1 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates
RootAge = <0.9 * safe constraint on root age, used if no fossil for root.
model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
alpha = 0.5 * alpha for gamma rates at sites
ncatG = 5 * No. categories in discrete gamma
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
BDparas = 1 1 0 * birth, death, sampling
kappa_gamma = 6 2 * gamma prior for kappa
alpha_gamma = 1 1 * gamma prior for alpha
rgene_gamma = 1 112 * gamma prior for overall rates for genes
sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3)
finetune = 1: 0.1 0.1 0.1 0.01 .5 * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr
print = 1
burnin = 25000000
sampfreq = 1000
nsample = 50000000