
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:46 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/chr2_11525.phylip" (19 taxa, 917 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: HKYG
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
HKYG	40	-3480.1636	7044.0715	0.3053	0.3053
GTRG	44	-3476.0145	7044.5702	0.2379	0.5432
GTRIG	45	-3474.9325	7044.6181	0.2323	0.7755
HKYIG	41	-3479.4490	7044.8340	0.2085	0.9840
GTRI	44	-3479.0266	7050.5945	0.0117	0.9957
HKYI	40	-3484.4266	7052.5975	0.0043	1.0000
K2PG	37	-3495.3263	7067.8518	0.0000	1.0000
K2PIG	38	-3494.6706	7068.7171	0.0000	1.0000
SYMG	41	-3493.3218	7072.5795	0.0000	1.0000
SYMIG	42	-3492.7474	7073.6276	0.0000	1.0000
K2PI	37	-3499.4803	7076.1596	0.0000	1.0000
SYMI	41	-3498.1249	7082.1857	0.0000	1.0000
F81G	39	-3541.3122	7164.1820	0.0000	1.0000
F81IG	40	-3540.3826	7164.5096	0.0000	1.0000
F81I	39	-3544.1306	7169.8187	0.0000	1.0000
JC69G	36	-3559.5358	7194.0989	0.0000	1.0000
JC69IG	37	-3558.8588	7194.9166	0.0000	1.0000
JC69I	36	-3563.1755	7201.3784	0.0000	1.0000
GTR	43	-3589.0023	7268.3391	0.0000	1.0000
HKY	39	-3594.7851	7271.1279	0.0000	1.0000
SYM	40	-3607.5992	7298.9427	0.0000	1.0000
K2P	36	-3611.9935	7299.0142	0.0000	1.0000
F81	38	-3654.1661	7387.7080	0.0000	1.0000
JC69	35	-3671.5753	7416.0110	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3474.9325	7039.8650	0.2969	0.2969
GTRG	44	-3476.0145	7040.0289	0.2735	0.5705
HKYG	40	-3480.1636	7040.3272	0.2356	0.8061
HKYIG	41	-3479.4490	7040.8980	0.1771	0.9832
GTRI	44	-3479.0266	7046.0532	0.0135	0.9967
HKYI	40	-3484.4266	7048.8532	0.0033	1.0000
K2PG	37	-3495.3263	7064.6527	0.0000	1.0000
K2PIG	38	-3494.6706	7065.3412	0.0000	1.0000
SYMG	41	-3493.3218	7068.6435	0.0000	1.0000
SYMIG	42	-3492.7474	7069.4949	0.0000	1.0000
K2PI	37	-3499.4803	7072.9606	0.0000	1.0000
SYMI	41	-3498.1249	7078.2497	0.0000	1.0000
F81G	39	-3541.3122	7160.6244	0.0000	1.0000
F81IG	40	-3540.3826	7160.7653	0.0000	1.0000
F81I	39	-3544.1306	7166.2611	0.0000	1.0000
JC69G	36	-3559.5358	7191.0717	0.0000	1.0000
JC69IG	37	-3558.8588	7191.7175	0.0000	1.0000
JC69I	36	-3563.1755	7198.3511	0.0000	1.0000
GTR	43	-3589.0023	7264.0046	0.0000	1.0000
HKY	39	-3594.7851	7267.5703	0.0000	1.0000
SYM	40	-3607.5992	7295.1984	0.0000	1.0000
K2P	36	-3611.9935	7295.9869	0.0000	1.0000
F81	38	-3654.1661	7384.3321	0.0000	1.0000
JC69	35	-3671.5753	7413.1506	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3480.1636	7233.1715	0.9179	0.9179
HKYIG	41	-3479.4490	7238.5634	0.0619	0.9798
HKYI	40	-3484.4266	7241.6975	0.0129	0.9928
K2PG	37	-3495.3263	7243.0337	0.0066	0.9994
K2PIG	38	-3494.6706	7248.5433	0.0004	0.9998
K2PI	37	-3499.4803	7251.3415	0.0001	0.9999
GTRG	44	-3476.0145	7252.1576	0.0001	1.0000
GTRIG	45	-3474.9325	7256.8148	0.0000	1.0000
GTRI	44	-3479.0266	7258.1819	0.0000	1.0000
SYMG	41	-3493.3218	7266.3089	0.0000	1.0000
SYMIG	42	-3492.7474	7271.9814	0.0000	1.0000
SYMI	41	-3498.1249	7275.9151	0.0000	1.0000
F81G	39	-3541.3122	7348.6476	0.0000	1.0000
F81IG	40	-3540.3826	7353.6096	0.0000	1.0000
F81I	39	-3544.1306	7354.2843	0.0000	1.0000
JC69G	36	-3559.5358	7364.6315	0.0000	1.0000
JC69IG	37	-3558.8588	7370.0985	0.0000	1.0000
JC69I	36	-3563.1755	7371.9109	0.0000	1.0000
HKY	39	-3594.7851	7455.5935	0.0000	1.0000
K2P	36	-3611.9935	7469.5468	0.0000	1.0000
GTR	43	-3589.0023	7471.3123	0.0000	1.0000
SYM	40	-3607.5992	7488.0427	0.0000	1.0000
F81	38	-3654.1661	7567.5342	0.0000	1.0000
JC69	35	-3671.5753	7581.8894	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11525.phylip = 1 - 917;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11525.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11525.phylip = 1 - 917;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11525.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;


[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/chr2_11525.phylip = 1 - 917;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11525.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

