
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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/chr10_4660.phylip" (19 taxa, 451 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1544.8735	3187.5007	0.4014	0.4014
HKYG	40	-1550.0638	3188.1276	0.2934	0.6948
GTRIG	45	-1544.8536	3189.9295	0.1192	0.8139
HKYIG	41	-1550.0331	3190.4868	0.0902	0.9041
K2PG	37	-1555.9124	3192.6335	0.0308	0.9350
GTRI	44	-1547.7997	3193.3532	0.0215	0.9565
HKYI	40	-1552.7639	3193.5279	0.0197	0.9762
K2PIG	38	-1555.9053	3195.0047	0.0094	0.9856
SYMG	41	-1552.6717	3195.7639	0.0064	0.9920
K2PI	37	-1557.7429	3196.2944	0.0049	0.9970
SYMIG	42	-1552.6689	3198.1907	0.0019	0.9989
SYMI	41	-1554.4821	3199.3847	0.0011	1.0000
GTR	43	-1555.8998	3207.0968	0.0000	1.0000
HKY	39	-1561.0310	3207.6533	0.0000	1.0000
K2P	36	-1566.1819	3210.7986	0.0000	1.0000
SYM	40	-1562.6134	3213.2268	0.0000	1.0000
F81G	39	-1596.7020	3278.9952	0.0000	1.0000
JC69G	36	-1600.5613	3279.5573	0.0000	1.0000
F81IG	40	-1596.7107	3281.4215	0.0000	1.0000
JC69IG	37	-1600.5614	3281.9315	0.0000	1.0000
F81I	39	-1598.2099	3282.0111	0.0000	1.0000
JC69I	36	-1602.0761	3282.5869	0.0000	1.0000
F81	38	-1605.4624	3294.1191	0.0000	1.0000
JC69	35	-1609.4348	3294.9418	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1544.8735	3177.7470	0.5240	0.5240
GTRIG	45	-1544.8536	3179.7072	0.1966	0.7206
HKYG	40	-1550.0638	3180.1276	0.1594	0.8800
HKYIG	41	-1550.0331	3182.0662	0.0605	0.9404
GTRI	44	-1547.7997	3183.5995	0.0281	0.9685
HKYI	40	-1552.7639	3185.5279	0.0107	0.9792
K2PG	37	-1555.9124	3185.8247	0.0092	0.9884
SYMG	41	-1552.6717	3187.3433	0.0043	0.9928
K2PIG	38	-1555.9053	3187.8105	0.0034	0.9962
SYMIG	42	-1552.6689	3189.3378	0.0016	0.9978
K2PI	37	-1557.7429	3189.4857	0.0015	0.9993
SYMI	41	-1554.4821	3190.9641	0.0007	1.0000
GTR	43	-1555.8998	3197.7995	0.0000	1.0000
HKY	39	-1561.0310	3200.0620	0.0000	1.0000
K2P	36	-1566.1819	3204.3639	0.0000	1.0000
SYM	40	-1562.6134	3205.2268	0.0000	1.0000
F81G	39	-1596.7020	3271.4039	0.0000	1.0000
JC69G	36	-1600.5613	3273.1225	0.0000	1.0000
F81IG	40	-1596.7107	3273.4215	0.0000	1.0000
F81I	39	-1598.2099	3274.4199	0.0000	1.0000
JC69IG	37	-1600.5614	3275.1228	0.0000	1.0000
JC69I	36	-1602.0761	3276.1521	0.0000	1.0000
F81	38	-1605.4624	3286.9249	0.0000	1.0000
JC69	35	-1609.4348	3288.8696	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1555.9124	3337.9490	0.8006	0.8006
K2PI	37	-1557.7429	3341.6100	0.1284	0.9289
K2PIG	38	-1555.9053	3344.0463	0.0380	0.9669
HKYG	40	-1550.0638	3344.5863	0.0290	0.9959
HKYI	40	-1552.7639	3349.9866	0.0019	0.9978
HKYIG	41	-1550.0331	3350.6364	0.0014	0.9992
K2P	36	-1566.1819	3352.3767	0.0006	0.9998
SYMG	41	-1552.6717	3355.9135	0.0001	0.9999
GTRG	44	-1544.8735	3358.6515	0.0000	1.0000
SYMI	41	-1554.4821	3359.5343	0.0000	1.0000
HKY	39	-1561.0310	3360.4092	0.0000	1.0000
SYMIG	42	-1552.6689	3362.0194	0.0000	1.0000
GTRI	44	-1547.7997	3364.5041	0.0000	1.0000
GTRIG	45	-1544.8536	3364.7233	0.0000	1.0000
SYM	40	-1562.6134	3369.6855	0.0000	1.0000
GTR	43	-1555.8998	3374.5926	0.0000	1.0000
JC69G	36	-1600.5613	3421.1354	0.0000	1.0000
JC69I	36	-1602.0761	3424.1649	0.0000	1.0000
JC69IG	37	-1600.5614	3427.2471	0.0000	1.0000
F81G	39	-1596.7020	3431.7512	0.0000	1.0000
JC69	35	-1609.4348	3432.7709	0.0000	1.0000
F81I	39	-1598.2099	3434.7671	0.0000	1.0000
F81IG	40	-1596.7107	3437.8802	0.0000	1.0000
F81	38	-1605.4624	3443.1606	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/chr10_4660.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4660.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/chr10_4660.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4660.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4660.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4660.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

