
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:58 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/chr8_1617.phylip" (19 taxa, 707 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	-2627.5653	5349.1125	0.9492	0.9492
HKYG	40	-2635.3643	5355.6535	0.0361	0.9852
HKYIG	41	-2635.3360	5357.8509	0.0120	0.9972
HKYI	40	-2638.0179	5360.9608	0.0025	0.9998
GTRIG	45	-2634.8680	5365.9992	0.0002	1.0000
GTRI	44	-2638.5247	5371.0312	0.0000	1.0000
GTR	43	-2665.8201	5423.3476	0.0000	1.0000
HKY	39	-2671.0834	5424.8444	0.0000	1.0000
K2PG	37	-2690.4448	5459.0928	0.0000	1.0000
K2PIG	38	-2690.3640	5461.1650	0.0000	1.0000
SYMG	41	-2688.1998	5463.5786	0.0000	1.0000
K2PI	37	-2693.4266	5465.0564	0.0000	1.0000
SYMIG	42	-2688.1195	5465.6788	0.0000	1.0000
SYMI	41	-2691.1444	5469.4678	0.0000	1.0000
F81G	39	-2714.3180	5511.3137	0.0000	1.0000
F81IG	40	-2719.1584	5523.2418	0.0000	1.0000
F81I	39	-2721.6602	5525.9981	0.0000	1.0000
K2P	36	-2727.5737	5531.1236	0.0000	1.0000
SYM	40	-2725.5086	5535.9422	0.0000	1.0000
F81	38	-2749.9335	5580.3041	0.0000	1.0000
JC69G	36	-2759.6299	5595.2358	0.0000	1.0000
JC69IG	37	-2759.5169	5597.2371	0.0000	1.0000
JC69I	36	-2762.0679	5600.1119	0.0000	1.0000
JC69	35	-2793.0275	5659.8105	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2627.5653	5343.1306	0.9683	0.9683
HKYG	40	-2635.3643	5350.7286	0.0217	0.9900
HKYIG	41	-2635.3360	5352.6719	0.0082	0.9982
HKYI	40	-2638.0179	5356.0359	0.0015	0.9997
GTRIG	45	-2634.8680	5359.7359	0.0002	1.0000
GTRI	44	-2638.5247	5365.0493	0.0000	1.0000
GTR	43	-2665.8201	5417.6402	0.0000	1.0000
HKY	39	-2671.0834	5420.1668	0.0000	1.0000
K2PG	37	-2690.4448	5454.8896	0.0000	1.0000
K2PIG	38	-2690.3640	5456.7279	0.0000	1.0000
SYMG	41	-2688.1998	5458.3997	0.0000	1.0000
SYMIG	42	-2688.1195	5460.2390	0.0000	1.0000
K2PI	37	-2693.4266	5460.8531	0.0000	1.0000
SYMI	41	-2691.1444	5464.2889	0.0000	1.0000
F81G	39	-2714.3180	5506.6361	0.0000	1.0000
F81IG	40	-2719.1584	5518.3169	0.0000	1.0000
F81I	39	-2721.6602	5521.3204	0.0000	1.0000
K2P	36	-2727.5737	5527.1474	0.0000	1.0000
SYM	40	-2725.5086	5531.0172	0.0000	1.0000
F81	38	-2749.9335	5575.8669	0.0000	1.0000
JC69G	36	-2759.6299	5591.2597	0.0000	1.0000
JC69IG	37	-2759.5169	5593.0338	0.0000	1.0000
JC69I	36	-2762.0679	5596.1358	0.0000	1.0000
JC69	35	-2793.0275	5656.0549	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2635.3643	5533.1698	0.8977	0.8977
HKYI	40	-2638.0179	5538.4771	0.0632	0.9609
HKYIG	41	-2635.3360	5539.6742	0.0347	0.9956
GTRG	44	-2627.5653	5543.8159	0.0044	1.0000
GTRIG	45	-2634.8680	5564.9823	0.0000	1.0000
GTRI	44	-2638.5247	5565.7347	0.0000	1.0000
HKY	39	-2671.0834	5598.0470	0.0000	1.0000
GTR	43	-2665.8201	5613.7645	0.0000	1.0000
K2PG	37	-2690.4448	5623.6477	0.0000	1.0000
K2PI	37	-2693.4266	5629.6112	0.0000	1.0000
K2PIG	38	-2690.3640	5630.0471	0.0000	1.0000
SYMG	41	-2688.1998	5645.4019	0.0000	1.0000
SYMI	41	-2691.1444	5651.2911	0.0000	1.0000
SYMIG	42	-2688.1195	5651.8023	0.0000	1.0000
F81G	39	-2714.3180	5684.5163	0.0000	1.0000
K2P	36	-2727.5737	5691.3445	0.0000	1.0000
F81I	39	-2721.6602	5699.2006	0.0000	1.0000
F81IG	40	-2719.1584	5700.7581	0.0000	1.0000
SYM	40	-2725.5086	5713.4585	0.0000	1.0000
F81	38	-2749.9335	5749.1861	0.0000	1.0000
JC69G	36	-2759.6299	5755.4568	0.0000	1.0000
JC69I	36	-2762.0679	5760.3329	0.0000	1.0000
JC69IG	37	-2759.5169	5761.7919	0.0000	1.0000
JC69	35	-2793.0275	5815.6910	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/chr8_1617.phylip = 1 - 707;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1617.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/chr8_1617.phylip = 1 - 707;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1617.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/chr8_1617.phylip = 1 - 707;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1617.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

