
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:53 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/chr7_10394.phylip" (19 taxa, 851 characters)

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


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	-3574.1376	7241.1884	0.5685	0.5685
GTRIG	45	-3573.2985	7241.7398	0.4315	1.0000
HKYIG	41	-3588.8359	7263.9289	0.0000	1.0000
HKYG	40	-3590.1143	7264.2780	0.0000	1.0000
GTRI	44	-3591.2209	7275.3550	0.0000	1.0000
HKYI	40	-3604.3413	7292.7319	0.0000	1.0000
SYMIG	42	-3605.2780	7299.0264	0.0000	1.0000
SYMG	41	-3606.7155	7299.6881	0.0000	1.0000
K2PIG	38	-3610.3258	7300.3019	0.0000	1.0000
K2PG	37	-3611.8756	7301.2101	0.0000	1.0000
SYMI	41	-3620.9738	7328.2046	0.0000	1.0000
K2PI	37	-3625.6422	7328.7431	0.0000	1.0000
F81IG	40	-3661.0924	7406.2341	0.0000	1.0000
F81G	39	-3662.6859	7407.2189	0.0000	1.0000
JC69IG	37	-3677.2677	7431.9942	0.0000	1.0000
JC69G	36	-3678.9655	7433.2036	0.0000	1.0000
F81I	39	-3676.4401	7434.7274	0.0000	1.0000
GTR	43	-3683.6071	7457.9031	0.0000	1.0000
JC69I	36	-3692.6825	7460.6377	0.0000	1.0000
HKY	39	-3696.9817	7475.8105	0.0000	1.0000
SYM	40	-3713.8791	7511.8076	0.0000	1.0000
K2P	36	-3719.5669	7514.4065	0.0000	1.0000
F81	38	-3767.7097	7615.0697	0.0000	1.0000
JC69	35	-3784.4587	7642.0095	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3574.1376	7236.2753	0.5401	0.5401
GTRIG	45	-3573.2985	7236.5969	0.4599	1.0000
HKYIG	41	-3588.8359	7259.6718	0.0000	1.0000
HKYG	40	-3590.1143	7260.2286	0.0000	1.0000
GTRI	44	-3591.2209	7270.4418	0.0000	1.0000
HKYI	40	-3604.3413	7288.6825	0.0000	1.0000
SYMIG	42	-3605.2780	7294.5561	0.0000	1.0000
SYMG	41	-3606.7155	7295.4310	0.0000	1.0000
K2PIG	38	-3610.3258	7296.6517	0.0000	1.0000
K2PG	37	-3611.8756	7297.7513	0.0000	1.0000
SYMI	41	-3620.9738	7323.9475	0.0000	1.0000
K2PI	37	-3625.6422	7325.2843	0.0000	1.0000
F81IG	40	-3661.0924	7402.1847	0.0000	1.0000
F81G	39	-3662.6859	7403.3718	0.0000	1.0000
JC69IG	37	-3677.2677	7428.5354	0.0000	1.0000
JC69G	36	-3678.9655	7429.9309	0.0000	1.0000
F81I	39	-3676.4401	7430.8803	0.0000	1.0000
GTR	43	-3683.6071	7453.2142	0.0000	1.0000
JC69I	36	-3692.6825	7457.3650	0.0000	1.0000
HKY	39	-3696.9817	7471.9634	0.0000	1.0000
SYM	40	-3713.8791	7507.7583	0.0000	1.0000
K2P	36	-3719.5669	7511.1337	0.0000	1.0000
F81	38	-3767.7097	7611.4195	0.0000	1.0000
JC69	35	-3784.4587	7638.9175	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3574.1376	7445.1174	0.8525	0.8525
HKYG	40	-3590.1143	7450.0851	0.0711	0.9236
GTRIG	45	-3573.2985	7450.1855	0.0676	0.9912
HKYIG	41	-3588.8359	7454.2747	0.0088	1.0000
K2PG	37	-3611.8756	7473.3685	0.0000	1.0000
K2PIG	38	-3610.3258	7477.0153	0.0000	1.0000
HKYI	40	-3604.3413	7478.5390	0.0000	1.0000
GTRI	44	-3591.2209	7479.2840	0.0000	1.0000
SYMG	41	-3606.7155	7490.0339	0.0000	1.0000
SYMIG	42	-3605.2780	7493.9054	0.0000	1.0000
K2PI	37	-3625.6422	7500.9016	0.0000	1.0000
SYMI	41	-3620.9738	7518.5504	0.0000	1.0000
F81G	39	-3662.6859	7588.4819	0.0000	1.0000
F81IG	40	-3661.0924	7592.0412	0.0000	1.0000
JC69G	36	-3678.9655	7600.8018	0.0000	1.0000
JC69IG	37	-3677.2677	7604.1527	0.0000	1.0000
F81I	39	-3676.4401	7615.9904	0.0000	1.0000
JC69I	36	-3692.6825	7628.2358	0.0000	1.0000
HKY	39	-3696.9817	7657.0735	0.0000	1.0000
GTR	43	-3683.6071	7657.3099	0.0000	1.0000
K2P	36	-3719.5669	7682.0046	0.0000	1.0000
SYM	40	-3713.8791	7697.6147	0.0000	1.0000
F81	38	-3767.7097	7791.7832	0.0000	1.0000
JC69	35	-3784.4587	7805.0419	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/chr7_10394.phylip = 1 - 851;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10394.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/chr7_10394.phylip = 1 - 851;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10394.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10394.phylip = 1 - 851;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10394.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;


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End of Output

