
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:11 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/chr1_28767.phylip" (19 taxa, 806 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-3108.4913	6310.1863	0.6254	0.6254
GTRIG	45	-3107.8831	6311.2136	0.3741	0.9995
HKYG	40	-3120.6022	6325.4920	0.0003	0.9998
HKYIG	41	-3120.0117	6326.5312	0.0002	1.0000
GTRI	44	-3119.0699	6331.3434	0.0000	1.0000
SYMG	41	-3125.8533	6338.2145	0.0000	1.0000
SYMIG	42	-3125.2095	6339.1530	0.0000	1.0000
HKYI	40	-3130.6958	6345.6792	0.0000	1.0000
K2PG	37	-3134.0789	6345.8192	0.0000	1.0000
K2PIG	38	-3133.4454	6346.7552	0.0000	1.0000
SYMI	41	-3136.5001	6359.5081	0.0000	1.0000
K2PI	37	-3143.9711	6365.6036	0.0000	1.0000
GTR	43	-3177.0304	6445.0266	0.0000	1.0000
F81G	39	-3182.1132	6446.2995	0.0000	1.0000
F81IG	40	-3181.6336	6447.5547	0.0000	1.0000
HKY	39	-3187.9809	6458.0348	0.0000	1.0000
F81I	39	-3191.2078	6464.4887	0.0000	1.0000
JC69G	36	-3197.9397	6471.3437	0.0000	1.0000
SYM	40	-3193.8750	6472.0375	0.0000	1.0000
JC69IG	37	-3197.4339	6472.5293	0.0000	1.0000
K2P	36	-3201.4900	6478.4443	0.0000	1.0000
JC69I	36	-3207.2571	6489.9784	0.0000	1.0000
F81	38	-3246.8137	6573.4917	0.0000	1.0000
JC69	35	-3262.8888	6599.0503	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3108.4913	6304.9826	0.5965	0.5965
GTRIG	45	-3107.8831	6305.7663	0.4031	0.9997
HKYG	40	-3120.6022	6321.2044	0.0002	0.9999
HKYIG	41	-3120.0117	6322.0233	0.0001	1.0000
GTRI	44	-3119.0699	6326.1398	0.0000	1.0000
SYMG	41	-3125.8533	6333.7066	0.0000	1.0000
SYMIG	42	-3125.2095	6334.4190	0.0000	1.0000
HKYI	40	-3130.6958	6341.3916	0.0000	1.0000
K2PG	37	-3134.0789	6342.1577	0.0000	1.0000
K2PIG	38	-3133.4454	6342.8908	0.0000	1.0000
SYMI	41	-3136.5001	6355.0002	0.0000	1.0000
K2PI	37	-3143.9711	6361.9422	0.0000	1.0000
GTR	43	-3177.0304	6440.0607	0.0000	1.0000
F81G	39	-3182.1132	6442.2264	0.0000	1.0000
F81IG	40	-3181.6336	6443.2671	0.0000	1.0000
HKY	39	-3187.9809	6453.9617	0.0000	1.0000
F81I	39	-3191.2078	6460.4156	0.0000	1.0000
SYM	40	-3193.8750	6467.7500	0.0000	1.0000
JC69G	36	-3197.9397	6467.8794	0.0000	1.0000
JC69IG	37	-3197.4339	6468.8678	0.0000	1.0000
K2P	36	-3201.4900	6474.9801	0.0000	1.0000
JC69I	36	-3207.2571	6486.5142	0.0000	1.0000
F81	38	-3246.8137	6569.6273	0.0000	1.0000
JC69	35	-3262.8888	6595.7776	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3120.6022	6508.8878	0.7163	0.7163
GTRG	44	-3108.4913	6511.4343	0.2005	0.9168
HKYIG	41	-3120.0117	6514.3988	0.0455	0.9623
K2PG	37	-3134.0789	6515.7648	0.0230	0.9853
GTRIG	45	-3107.8831	6516.9100	0.0130	0.9983
K2PIG	38	-3133.4454	6521.1900	0.0015	0.9998
SYMG	41	-3125.8533	6526.0820	0.0001	1.0000
HKYI	40	-3130.6958	6529.0750	0.0000	1.0000
SYMIG	42	-3125.2095	6531.4865	0.0000	1.0000
GTRI	44	-3119.0699	6532.5914	0.0000	1.0000
K2PI	37	-3143.9711	6535.5493	0.0000	1.0000
SYMI	41	-3136.5001	6547.3757	0.0000	1.0000
F81G	39	-3182.1132	6625.2176	0.0000	1.0000
F81IG	40	-3181.6336	6630.9505	0.0000	1.0000
JC69G	36	-3197.9397	6636.7945	0.0000	1.0000
HKY	39	-3187.9809	6636.9530	0.0000	1.0000
GTR	43	-3177.0304	6641.8203	0.0000	1.0000
JC69IG	37	-3197.4339	6642.4749	0.0000	1.0000
F81I	39	-3191.2078	6643.4069	0.0000	1.0000
K2P	36	-3201.4900	6643.8951	0.0000	1.0000
JC69I	36	-3207.2571	6655.4292	0.0000	1.0000
SYM	40	-3193.8750	6655.4333	0.0000	1.0000
F81	38	-3246.8137	6747.9265	0.0000	1.0000
JC69	35	-3262.8888	6760.0005	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/chr1_28767.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28767.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/chr1_28767.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28767.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28767.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28767.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

