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EthanIce

新虫 (初入文坛)

应助: 0 (幼儿园)
金币: 8
帖子: 4
在线: 1.4小时
虫号: 3366566
注册: 2014-08-14
专业: 微生物资源与分类学

[求助] PAML branch-site 的结果分析

TREE #  1:  (((((6, 7, 8), 9), 5), (((10, 11), 12), 13, (14, (15, 16)))), (((1, 2), 3), 4), (17, (18, 19))); MP score: 83
lnL(ntime: 33  np: 38):  -1035.533929    +0.000000
  20..21 21..22 22..23 23..24 24..6 24..7 24..8 23..9 22..5 21..25 25..26 26..27 27..10 27..11 26..12 25..13 25..28 28..14 28..29 29..15 29..16 20..30 30..31 31..32 32..1 32..2 31..3 30..4 20..33 33..17 33..34 34..18 34..19
0.042333 0.075622 0.026519 0.008018 0.007767 0.000004 0.023339 0.007530 0.037779 0.023589 0.000004 0.000004 0.007956 0.000004 0.007935 0.016006 0.008104 0.016154 0.007906 0.016186 0.008059 0.069643 0.006258 0.008004 0.015965 0.000004 0.000004 0.034475 0.135219 0.027063 0.000004 0.032959 0.040867 4.154928 0.326513 0.269308 0.000001 4.809777

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length = 0.71128

(((((6: 0.007767, 7: 0.000004, 8: 0.023339): 0.008018, 9: 0.007530): 0.026519, 5: 0.037779): 0.075622, (((10: 0.007956, 11: 0.000004): 0.000004, 12: 0.007935): 0.000004, 13: 0.016006, (14: 0.016154, (15: 0.016186, 16: 0.008059): 0.007906): 0.008104): 0.023589): 0.042333, (((1: 0.015965, 2: 0.000004): 0.008004, 3: 0.000004): 0.006258, 4: 0.034475): 0.069643, (17: 0.027063, (18: 0.032959, 19: 0.040867): 0.000004): 0.135219);

(((((6.langur_Sen&Sve: 0.007767, 7.langur_Tob&Tfr: 0.000004, 8.Douc_langur_Pne: 0.023339): 0.008018, 9.probiscis_Nla: 0.007530): 0.026519, 5.colobus_Cgu&Can: 0.037779): 0.075622, (((10.baboon_Pcy: 0.007956, 11.mangabey_Cat: 0.000004): 0.000004, 12.rhesus_Mmu: 0.007935): 0.000004, 13.Allen_Ani: 0.016006, (14.talapoin_Mta: 0.016154, (15.patas_Epa: 0.016186, 16.vervet_Cae: 0.008059): 0.007906): 0.008104): 0.023589): 0.042333, (((1.human: 0.015965, 2.chimp_bonobo_gorilla: 0.000004): 0.008004, 3.orangutan_Ppy: 0.000004): 0.006258, 4.gibbon_Ggo: 0.034475): 0.069643, (17.squirrel_m: 0.027063, (18.tamarin_Soe: 0.032959, 19.Marmoset_Cja: 0.040867): 0.000004): 0.135219);

Detailed output identifying parameters

kappa (ts/tv) =  4.15493

dN/dS (w) for site classes (K=4)

site class          0       1    2a    2b
proportion    0.32651  0.26931  0.22149  0.18269
background w    0.00000  1.00000  0.00000  1.00000
foreground w    0.00000  1.00000  4.80978  4.80978

Naive Empirical Bayes (NEB) analysis (please use the BEB results.)
Positive sites for foreground lineages Prob(w>1):

14 R 0.917
21 R 0.912
23 I 0.904
37 G 0.562
41 R 0.754
50 R 0.741
62 R 0.582
87 D 0.932
126 Q 0.728

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positive sites for foreground lineages Prob(w>1):
14 R 0.859
21 R 0.858
23 I 0.853
37 G 0.510
41 R 0.710
50 R 0.704
62 R 0.564
87 D 0.869
126 Q 0.710

The grid (see ternary graph for p0-p1)

w0: 0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2: 1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500

Posterior on the grid

w0: 0.619  0.277  0.081  0.019  0.004  0.001  0.000  0.000  0.000  0.000
w2: 0.031  0.089  0.125  0.133  0.128  0.118  0.108  0.098  0.089  0.081

Posterior for p0-p1 (see the ternary graph)

0.000
0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.001 0.001
0.000 0.000 0.000 0.000 0.001 0.002 0.011 0.010 0.020 0.007 0.004
0.000 0.000 0.000 0.000 0.005 0.008 0.036 0.037 0.066 0.047 0.037 0.011 0.002
0.000 0.000 0.001 0.002 0.023 0.027 0.060 0.067 0.063 0.069 0.039 0.033 0.012 0.004 0.001
0.000 0.000 0.015 0.018 0.036 0.044 0.022 0.035 0.013 0.023 0.008 0.013 0.005 0.005 0.001 0.001 0.000
0.011 0.012 0.003 0.014 0.001 0.004 0.001 0.002 0.000 0.002 0.000 0.001 0.000 0.001 0.000 0.000 0.000 0.000 0.000

sum of density on p0-p1 = 1.000000

Time used:  3:06

根据说明文档，跑的example/lysomzyme/lsomzymeLarge.ctl，得到的结果文件如何解释？

前景枝的dn/ds到底等于多少啊？

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