
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:04 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip" (19 taxa, 397 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRG	44	-1019.6370	2138.5240	0.3970	0.3970
GTRI	44	-1019.7142	2138.6785	0.3675	0.7646
HKYG	40	-1026.4059	2142.0253	0.0690	0.8335
HKYI	40	-1026.7744	2142.7623	0.0477	0.8812
GTRIG	45	-1020.5451	2142.8850	0.0449	0.9261
K2PG	37	-1030.8611	2143.5550	0.0321	0.9582
HKYIG	41	-1026.2741	2144.2496	0.0227	0.9808
SYMG	41	-1027.2941	2146.2896	0.0082	0.9890
K2PI	37	-1032.6633	2147.1595	0.0053	0.9943
K2PIG	38	-1031.8800	2148.0394	0.0034	0.9977
SYMI	41	-1029.0515	2149.8044	0.0014	0.9991
SYMIG	42	-1028.2909	2150.7852	0.0009	1.0000
F81G	39	-1037.1393	2161.0182	0.0000	1.0000
F81I	39	-1037.3728	2161.4850	0.0000	1.0000
GTR	43	-1033.0240	2162.7676	0.0000	1.0000
JC69G	36	-1041.8890	2163.1781	0.0000	1.0000
F81IG	40	-1038.0614	2165.3363	0.0000	1.0000
HKY	39	-1039.8135	2166.3665	0.0000	1.0000
JC69I	36	-1043.7593	2166.9185	0.0000	1.0000
JC69IG	37	-1042.9530	2167.7389	0.0000	1.0000
K2P	36	-1045.6260	2170.6521	0.0000	1.0000
SYM	40	-1040.9033	2171.0201	0.0000	1.0000
F81	38	-1051.0251	2186.3295	0.0000	1.0000
JC69	35	-1056.2868	2189.5541	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1019.6370	2127.2740	0.4468	0.4468
GTRI	44	-1019.7142	2127.4285	0.4136	0.8605
GTRIG	45	-1020.5451	2131.0901	0.0663	0.9268
HKYG	40	-1026.4059	2132.8118	0.0280	0.9548
HKYI	40	-1026.7744	2133.5488	0.0194	0.9742
HKYIG	41	-1026.2741	2134.5482	0.0118	0.9860
K2PG	37	-1030.8611	2135.7221	0.0065	0.9925
SYMG	41	-1027.2941	2136.5882	0.0042	0.9967
K2PI	37	-1032.6633	2139.3266	0.0011	0.9978
K2PIG	38	-1031.8800	2139.7601	0.0009	0.9987
SYMI	41	-1029.0515	2140.1030	0.0007	0.9994
SYMIG	42	-1028.2909	2140.5818	0.0006	1.0000
GTR	43	-1033.0240	2152.0481	0.0000	1.0000
F81G	39	-1037.1393	2152.2787	0.0000	1.0000
F81I	39	-1037.3728	2152.7455	0.0000	1.0000
JC69G	36	-1041.8890	2155.7781	0.0000	1.0000
F81IG	40	-1038.0614	2156.1228	0.0000	1.0000
HKY	39	-1039.8135	2157.6270	0.0000	1.0000
JC69I	36	-1043.7593	2159.5185	0.0000	1.0000
JC69IG	37	-1042.9530	2159.9061	0.0000	1.0000
SYM	40	-1040.9033	2161.8066	0.0000	1.0000
K2P	36	-1045.6260	2163.2521	0.0000	1.0000
F81	38	-1051.0251	2178.0501	0.0000	1.0000
JC69	35	-1056.2868	2182.5735	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1030.8611	2283.1278	0.8314	0.8314
K2PI	37	-1032.6633	2286.7322	0.1371	0.9685
K2PIG	38	-1031.8800	2291.1496	0.0151	0.9835
HKYG	40	-1026.4059	2292.1692	0.0090	0.9926
HKYI	40	-1026.7744	2292.9063	0.0063	0.9988
HKYIG	41	-1026.2741	2297.8896	0.0005	0.9994
JC69G	36	-1041.8890	2299.1998	0.0003	0.9996
SYMG	41	-1027.2941	2299.9296	0.0002	0.9998
GTRG	44	-1019.6370	2302.5672	0.0000	0.9999
GTRI	44	-1019.7142	2302.7217	0.0000	0.9999
JC69I	36	-1043.7593	2302.9402	0.0000	0.9999
SYMI	41	-1029.0515	2303.4444	0.0000	1.0000
K2P	36	-1045.6260	2306.6738	0.0000	1.0000
JC69IG	37	-1042.9530	2307.3117	0.0000	1.0000
F81G	39	-1037.1393	2307.6522	0.0000	1.0000
SYMIG	42	-1028.2909	2307.9071	0.0000	1.0000
F81I	39	-1037.3728	2308.1191	0.0000	1.0000
GTRIG	45	-1020.5451	2310.3673	0.0000	1.0000
HKY	39	-1039.8135	2313.0005	0.0000	1.0000
F81IG	40	-1038.0614	2315.4803	0.0000	1.0000
SYM	40	-1040.9033	2321.1641	0.0000	1.0000
JC69	35	-1056.2868	2322.0113	0.0000	1.0000
GTR	43	-1033.0240	2323.3573	0.0000	1.0000
F81	38	-1051.0251	2329.4397	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip = 1 - 397;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip = 1 - 397;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip = 1 - 397;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6328.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


-------------------------------------------------------------
End of Output

