
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:46 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/chr5_10251.phylip" (19 taxa, 1090 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-3590.2643	7265.8148	0.6507	0.6507
HKYG	40	-3592.2336	7267.5939	0.2673	0.9180
GTRIG	45	-3588.3974	7270.7604	0.0549	0.9728
GTRG	44	-3590.2759	7272.3412	0.0249	0.9977
HKYI	40	-3597.0644	7277.2555	0.0021	0.9999
GTRI	44	-3595.6076	7283.0047	0.0001	1.0000
K2PIG	38	-3632.5426	7343.9055	0.0000	1.0000
K2PG	37	-3634.7787	7346.2303	0.0000	1.0000
SYMIG	42	-3631.3599	7350.1697	0.0000	1.0000
SYMG	41	-3633.6991	7352.6845	0.0000	1.0000
K2PI	37	-3639.1898	7355.0526	0.0000	1.0000
SYMI	41	-3638.1911	7361.6685	0.0000	1.0000
F81IG	40	-3686.8830	7456.8928	0.0000	1.0000
F81G	39	-3688.2659	7457.5032	0.0000	1.0000
F81I	39	-3692.1740	7465.3195	0.0000	1.0000
HKY	39	-3695.3088	7471.5890	0.0000	1.0000
GTR	43	-3694.3712	7478.3599	0.0000	1.0000
JC69IG	37	-3720.1259	7516.9247	0.0000	1.0000
JC69G	36	-3721.5679	7517.6657	0.0000	1.0000
JC69I	36	-3725.4455	7525.4209	0.0000	1.0000
K2P	36	-3735.7995	7546.1289	0.0000	1.0000
SYM	40	-3734.8776	7552.8819	0.0000	1.0000
F81	38	-3781.8678	7642.5558	0.0000	1.0000
JC69	35	-3814.9554	7702.3017	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-3590.2643	7262.5286	0.6450	0.6450
HKYG	40	-3592.2336	7264.4672	0.2447	0.8897
GTRIG	45	-3588.3974	7266.7948	0.0764	0.9661
GTRG	44	-3590.2759	7268.5517	0.0317	0.9979
HKYI	40	-3597.0644	7274.1287	0.0020	0.9998
GTRI	44	-3595.6076	7279.2152	0.0002	1.0000
K2PIG	38	-3632.5426	7341.0853	0.0000	1.0000
K2PG	37	-3634.7787	7343.5573	0.0000	1.0000
SYMIG	42	-3631.3599	7346.7199	0.0000	1.0000
SYMG	41	-3633.6991	7349.3983	0.0000	1.0000
K2PI	37	-3639.1898	7352.3796	0.0000	1.0000
SYMI	41	-3638.1911	7358.3823	0.0000	1.0000
F81IG	40	-3686.8830	7453.7660	0.0000	1.0000
F81G	39	-3688.2659	7454.5318	0.0000	1.0000
F81I	39	-3692.1740	7462.3480	0.0000	1.0000
HKY	39	-3695.3088	7468.6175	0.0000	1.0000
GTR	43	-3694.3712	7474.7423	0.0000	1.0000
JC69IG	37	-3720.1259	7514.2517	0.0000	1.0000
JC69G	36	-3721.5679	7515.1358	0.0000	1.0000
JC69I	36	-3725.4455	7522.8910	0.0000	1.0000
K2P	36	-3735.7995	7543.5990	0.0000	1.0000
SYM	40	-3734.8776	7549.7551	0.0000	1.0000
F81	38	-3781.8678	7639.7356	0.0000	1.0000
JC69	35	-3814.9554	7699.9108	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3592.2336	7464.2245	0.8163	0.8163
HKYIG	41	-3590.2643	7467.2798	0.1772	0.9935
HKYI	40	-3597.0644	7473.8860	0.0065	1.0000
GTRG	44	-3590.2759	7488.2848	0.0000	1.0000
GTRIG	45	-3588.3974	7491.5218	0.0000	1.0000
GTRI	44	-3595.6076	7498.9482	0.0000	1.0000
K2PG	37	-3634.7787	7528.3329	0.0000	1.0000
K2PIG	38	-3632.5426	7530.8547	0.0000	1.0000
K2PI	37	-3639.1898	7537.1551	0.0000	1.0000
SYMG	41	-3633.6991	7554.1495	0.0000	1.0000
SYMIG	42	-3631.3599	7556.4651	0.0000	1.0000
SYMI	41	-3638.1911	7563.1335	0.0000	1.0000
F81G	39	-3688.2659	7649.2952	0.0000	1.0000
F81IG	40	-3686.8830	7653.5233	0.0000	1.0000
F81I	39	-3692.1740	7657.1114	0.0000	1.0000
HKY	39	-3695.3088	7663.3809	0.0000	1.0000
GTR	43	-3694.3712	7689.4815	0.0000	1.0000
JC69G	36	-3721.5679	7694.9174	0.0000	1.0000
JC69IG	37	-3720.1259	7699.0273	0.0000	1.0000
JC69I	36	-3725.4455	7702.6726	0.0000	1.0000
K2P	36	-3735.7995	7723.3806	0.0000	1.0000
SYM	40	-3734.8776	7749.5124	0.0000	1.0000
F81	38	-3781.8678	7829.5051	0.0000	1.0000
JC69	35	-3814.9554	7874.6984	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10251.phylip = 1 - 1090;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10251.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10251.phylip = 1 - 1090;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10251.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr5_10251.phylip = 1 - 1090;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10251.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;


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End of Output

