
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:06 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_28709.phylip" (19 taxa, 579 characters)

Minimum AIC  model: HKYG
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	-1460.8057	3007.7081	0.3994	0.3994
HKYI	40	-1460.8567	3007.8100	0.3796	0.7790
HKYIG	41	-1460.7663	3009.9461	0.1305	0.9095
GTRG	44	-1458.4587	3012.3331	0.0396	0.9490
GTRI	44	-1458.5361	3012.4879	0.0366	0.9857
GTRIG	45	-1458.4088	3014.5850	0.0128	0.9985
HKY	39	-1467.5876	3018.9638	0.0014	0.9999
GTR	43	-1465.7724	3024.6177	0.0001	1.0000
K2PI	37	-1480.6958	3040.5893	0.0000	1.0000
K2PG	37	-1480.7037	3040.6052	0.0000	1.0000
K2PIG	38	-1480.6921	3042.8731	0.0000	1.0000
SYMI	41	-1480.1760	3048.7653	0.0000	1.0000
SYMG	41	-1480.1957	3048.8048	0.0000	1.0000
SYMIG	42	-1480.1855	3051.1098	0.0000	1.0000
K2P	36	-1487.1294	3051.1740	0.0000	1.0000
SYM	40	-1486.6381	3059.3728	0.0000	1.0000
F81I	39	-1492.1385	3068.0655	0.0000	1.0000
F81G	39	-1492.1722	3068.1330	0.0000	1.0000
F81IG	40	-1492.1431	3070.3829	0.0000	1.0000
F81	38	-1498.0288	3077.5464	0.0000	1.0000
JC69I	36	-1509.0360	3094.9871	0.0000	1.0000
JC69G	36	-1509.0887	3095.0924	0.0000	1.0000
JC69IG	37	-1509.0621	3097.3221	0.0000	1.0000
JC69	35	-1514.8977	3104.4363	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1460.8057	3001.6115	0.3598	0.3598
HKYI	40	-1460.8567	3001.7133	0.3419	0.7018
HKYIG	41	-1460.7663	3003.5327	0.1377	0.8395
GTRG	44	-1458.4587	3004.9173	0.0689	0.9084
GTRI	44	-1458.5361	3005.0722	0.0638	0.9721
GTRIG	45	-1458.4088	3006.8177	0.0266	0.9988
HKY	39	-1467.5876	3013.1753	0.0011	0.9999
GTR	43	-1465.7724	3017.5448	0.0001	1.0000
K2PI	37	-1480.6958	3035.3915	0.0000	1.0000
K2PG	37	-1480.7037	3035.4074	0.0000	1.0000
K2PIG	38	-1480.6921	3037.3842	0.0000	1.0000
SYMI	41	-1480.1760	3042.3519	0.0000	1.0000
SYMG	41	-1480.1957	3042.3914	0.0000	1.0000
SYMIG	42	-1480.1855	3044.3710	0.0000	1.0000
K2P	36	-1487.1294	3046.2589	0.0000	1.0000
SYM	40	-1486.6381	3053.2762	0.0000	1.0000
F81I	39	-1492.1385	3062.2770	0.0000	1.0000
F81G	39	-1492.1722	3062.3445	0.0000	1.0000
F81IG	40	-1492.1431	3064.2862	0.0000	1.0000
F81	38	-1498.0288	3072.0575	0.0000	1.0000
JC69I	36	-1509.0360	3090.0719	0.0000	1.0000
JC69G	36	-1509.0887	3090.1773	0.0000	1.0000
JC69IG	37	-1509.0621	3092.1243	0.0000	1.0000
JC69	35	-1514.8977	3099.7954	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1460.8057	3176.0636	0.4948	0.4948
HKYI	40	-1460.8567	3176.1654	0.4702	0.9650
HKYIG	41	-1460.7663	3182.3461	0.0214	0.9864
HKY	39	-1467.5876	3183.2661	0.0135	0.9999
K2PI	37	-1480.6958	3196.7597	0.0000	1.0000
K2PG	37	-1480.7037	3196.7756	0.0000	1.0000
GTRG	44	-1458.4587	3196.8146	0.0000	1.0000
GTRI	44	-1458.5361	3196.9695	0.0000	1.0000
GTRIG	45	-1458.4088	3203.0763	0.0000	1.0000
K2PIG	38	-1480.6921	3203.1137	0.0000	1.0000
K2P	36	-1487.1294	3203.2658	0.0000	1.0000
GTR	43	-1465.7724	3205.0808	0.0000	1.0000
SYMI	41	-1480.1760	3221.1653	0.0000	1.0000
SYMG	41	-1480.1957	3221.2048	0.0000	1.0000
SYMIG	42	-1480.1855	3227.5457	0.0000	1.0000
SYM	40	-1486.6381	3227.7283	0.0000	1.0000
F81I	39	-1492.1385	3232.3678	0.0000	1.0000
F81G	39	-1492.1722	3232.4353	0.0000	1.0000
F81	38	-1498.0288	3237.7870	0.0000	1.0000
F81IG	40	-1492.1431	3238.7383	0.0000	1.0000
JC69I	36	-1509.0360	3247.0788	0.0000	1.0000
JC69G	36	-1509.0887	3247.1842	0.0000	1.0000
JC69	35	-1514.8977	3252.4410	0.0000	1.0000
JC69IG	37	-1509.0621	3253.4925	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28709.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28709.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28709.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28709.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/chr1_28709.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28709.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

