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seed used = 785596301
Data set 1
3 141
all_s57600 CTC TTC CAC ACC TCC CAC TCC CCC CCC CTC CAC TCC TTC TTC ACC TCC CCT TCC CCC TCC CTC CTT CCC TCC CCC ACC CTC TTC CTT TTC CCC TTC CAC TCC CCC TTC CTC CGC CTC CCC TCC CTC CCC CCC CAC CAC CCC
all_s56012 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CTC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC
all_c11513 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CCC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC
Printing out site pattern counts
11 93 P
all_s57600 ACC CAC CAC CAC CAC CCC CCC CCC CCC CCC CCC CCT CGC CTC CTC CTC CTC CTC CTC CTT CTT TCC TCC TCC TCC TCC TCC TCC TTC TTC TTC
all_s56012 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... ... ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ...
all_c11513 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... .C. ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ...
3 3 1 1 1 1 5 1 1 1 2 1 1 1 1
2 1 1 1 1 1 1 1 1 1 3 1 1 1 5
1
CODONML (in paml version 4.4, January 2010) /scratch/davepaml17/cluster45_fake.phy
Model: One dN/dS ratio for branches Global clock
Codon frequency model: F3x4
ns = 3 ls = 47
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 1 0 0 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 0 | Cys TGT 0 0 0 0 0 0
TTC 7 7 7 7 9 7 | TCC 9 10 8 10 8 9 | TAC 0 0 0 0 0 0 | TGC 0 0 0 0 0 0
Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 0 0 0 0 0 0 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------
Leu CTT 2 1 1 2 1 0 | Pro CCT 1 0 0 0 0 0 | His CAT 0 0 0 0 0 0 | Arg CGT 0 0 0 0 1 0
CTC 7 9 4 6 8 10 | CCC 11 11 19 12 13 12 | CAC 6 5 4 5 4 5 | CGC 1 1 1 0 0 1
CTA 0 0 0 0 0 0 | CCA 0 0 0 0 0 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0
CTG 0 0 0 0 0 0 | CCG 0 0 0 0 0 0 | CAG 0 0 0 0 0 0 | CGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 0 0 0 0 0 0 | Thr ACT 0 0 0 0 0 0 | Asn AAT 0 0 0 0 0 0 | Ser AGT 0 0 0 0 0 0
ATC 0 0 0 0 0 0 | ACC 3 3 3 4 3 3 | AAC 0 0 0 0 0 0 | AGC 0 0 0 0 0 0
ATA 0 0 0 0 0 0 | ACA 0 0 0 0 0 0 | Lys AAA 0 0 0 0 0 0 | Arg AGA 0 0 0 0 0 0
Met ATG 0 0 0 0 0 0 | ACG 0 0 0 0 0 0 | AAG 0 0 0 0 0 0 | AGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------
Val GTT 0 0 0 0 0 0 | Ala GCT 0 0 0 0 0 0 | Asp GAT 0 0 0 0 0 0 | Gly GGT 0 0 0 0 0 0
GTC 0 0 0 0 0 0 | GCC 0 0 0 0 0 0 | GAC 0 0 0 0 0 0 | GGC 0 0 0 0 0 0
GTA 0 0 0 0 0 0 | GCA 0 0 0 0 0 0 | Glu GAA 0 0 0 0 0 0 | GGA 0 0 0 0 0 0
GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 | Ser TCT 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 | Cys TGT 0 0 0 0 0
TTC 7 8 9 7 7 | TCC 9 12 9 10 10 | TAC 0 0 0 0 0 | TGC 0 0 0 0 0
Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 0 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 0 0 0 0 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Leu CTT 0 1 1 1 1 | Pro CCT 0 0 1 0 0 | His CAT 0 0 1 0 0 | Arg CGT 0 0 0 0 0
CTC 9 8 6 9 9 | CCC 13 8 11 11 11 | CAC 5 5 5 5 5 | CGC 1 1 0 1 1
CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 0 0 0 0 0 | CGA 0 0 0 0 0
CTG 0 0 0 0 0 | CCG 0 0 0 0 0 | CAG 0 0 0 0 0 | CGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 0 0 0 0 0 | Thr ACT 0 0 0 0 0 | Asn AAT 0 0 0 0 0 | Ser AGT 0 0 0 0 0
ATC 0 0 0 0 0 | ACC 3 4 4 3 3 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0
ATA 0 0 0 0 0 | ACA 0 0 0 0 0 | Lys AAA 0 0 0 0 0 | Arg AGA 0 0 0 0 0
Met ATG 0 0 0 0 0 | ACG 0 0 0 0 0 | AAG 0 0 0 0 0 | AGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Val GTT 0 0 0 0 0 | Ala GCT 0 0 0 0 0 | Asp GAT 0 0 0 0 0 | Gly GGT 0 0 0 0 0
GTC 0 0 0 0 0 | GCC 0 0 0 0 0 | GAC 0 0 0 0 0 | GGC 0 0 0 0 0
GTA 0 0 0 0 0 | GCA 0 0 0 0 0 | Glu GAA 0 0 0 0 0 | GGA 0 0 0 0 0
GTG 0 0 0 0 0 | GCG 0 0 0 0 0 | GAG 0 0 0 0 0 | GGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: all_s57600
position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
position 2: T:0.34043 C:0.51064 A:0.12766 G:0.02128
position 3: T:0.06383 C:0.93617 A:0.00000 G:0.00000
Average T:0.24823 C:0.68085 A:0.06383 G:0.00709
#2: all_s56012
position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
position 2: T:0.36170 C:0.51064 A:0.10638 G:0.02128
position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000
Average T:0.23404 C:0.70213 A:0.05674 G:0.00709
#3: all_c11513
position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
position 2: T:0.34043 C:0.53191 A:0.10638 G:0.02128
position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000
Average T:0.22695 C:0.70922 A:0.05674 G:0.00709
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 1 | Ser S TCT 0 | Tyr Y TAT 0 | Cys C TGT 0
TTC 82 | TCC 104 | TAC 0 | TGC 0
Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 11 | Pro P CCT 2 | His H CAT 1 | Arg R CGT 1
CTC 85 | CCC 132 | CAC 54 | CGC 8
CTA 0 | CCA 0 | Gln Q CAA 0 | CGA 0
CTG 0 | CCG 0 | CAG 0 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0
ATC 0 | ACC 36 | AAC 0 | AGC 0
ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0
Met M ATG 0 | ACG 0 | AAG 0 | AGG 0
------------------------------------------------------------------------------
Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
GTC 0 | GCC 0 | GAC 0 | GGC 0
GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0
GTG 0 | GCG 0 | GAG 0 | GGG 0
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.36170 C:0.56867 A:0.06963 G:0.00000
position 2: T:0.34623 C:0.52998 A:0.10638 G:0.01741
position 3: T:0.03095 C:0.96905 A:0.00000 G:0.00000
Average T:0.24629 C:0.68923 A:0.05867 G:0.00580
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.00387564 0.12135585 0.00000000 0.00000000
0.00593254 0.18576259 0.00000000 0.00000000
0.00119084 0.03728811 0.00000000 0.00000000
0.00019486 0.00610169 0.00000000 0.00000000
0.00609325 0.19079477 0.00000000 0.00000000
0.00932709 0.29205456 0.00000000 0.00000000
0.00187223 0.05862409 0.00000000 0.00000000
0.00030636 0.00959303 0.00000000 0.00000000
0.00074611 0.02336262 0.00000000 0.00000000
0.00114209 0.03576178 0.00000000 0.00000000
0.00022925 0.00717846 0.00000000 0.00000000
0.00003751 0.00117466 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
all_s57600
all_s56012 0.8758 (0.0717 0.0819)
all_c11513 1.0080 (0.0826 0.0819) 0.7616 (0.0199 0.0261)
pairwise comparison, codon frequencies: F3x4.
2 (all_c56012) ... 1 (all_s57600)
lnL = -126.880601
0.19045 2.92330 0.10941
t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353
3 (all_c11513) ... 1 (all_c57600)
lnL = -142.636697
4.21113 0.72684 0.00175
t= 4.2111 S= 4.2 N= 136.8 dN/dS= 0.0018 dN= 0.0789 dS=44.9635
3 (all_c11513) ... 2 (all_s56012)
lnL = -93.410530
0.02176 999.00000 0.13702
t= 0.0218 S= 0.0 N= 141.0 dN/dS= 0.1370 dN= 0.0073 dS= nan
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