
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:02 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/chr7_10870.phylip" (19 taxa, 438 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	-1543.9278	3185.9320	0.5471	0.5471
HKYG	40	-1549.9854	3188.2328	0.1732	0.7203
GTRIG	45	-1543.9303	3188.4218	0.1575	0.8778
HKYIG	41	-1549.9891	3190.6751	0.0511	0.9289
GTRI	44	-1546.3690	3190.8144	0.0476	0.9765
HKYI	40	-1551.9914	3192.2447	0.0233	0.9998
GTR	43	-1553.4342	3202.4725	0.0001	0.9999
HKY	39	-1559.3292	3204.4975	0.0001	1.0000
F81G	39	-1592.5854	3271.0099	0.0000	1.0000
K2PG	37	-1595.3317	3271.6935	0.0000	1.0000
F81IG	40	-1592.5840	3273.4300	0.0000	1.0000
F81I	39	-1594.0333	3273.9058	0.0000	1.0000
K2PIG	38	-1595.3130	3274.0546	0.0000	1.0000
K2PI	37	-1596.9864	3275.0027	0.0000	1.0000
SYMG	41	-1594.2639	3279.2247	0.0000	1.0000
SYMIG	42	-1594.2474	3281.6390	0.0000	1.0000
SYMI	41	-1595.9740	3282.6449	0.0000	1.0000
F81	38	-1601.7793	3286.9871	0.0000	1.0000
K2P	36	-1606.1019	3290.8472	0.0000	1.0000
SYM	40	-1604.6613	3297.5845	0.0000	1.0000
JC69G	36	-1629.4119	3337.4672	0.0000	1.0000
JC69IG	37	-1629.4075	3339.8450	0.0000	1.0000
JC69I	36	-1630.7845	3340.2124	0.0000	1.0000
JC69	35	-1639.2656	3354.7999	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1543.9278	3175.8557	0.6075	0.6075
GTRIG	45	-1543.9303	3177.8606	0.2229	0.8305
HKYG	40	-1549.9854	3179.9709	0.0776	0.9081
GTRI	44	-1546.3690	3180.7381	0.0529	0.9610
HKYIG	41	-1549.9891	3181.9782	0.0284	0.9894
HKYI	40	-1551.9914	3183.9828	0.0104	0.9999
GTR	43	-1553.4342	3192.8685	0.0001	1.0000
HKY	39	-1559.3292	3196.6583	0.0000	1.0000
F81G	39	-1592.5854	3263.1707	0.0000	1.0000
K2PG	37	-1595.3317	3264.6635	0.0000	1.0000
F81IG	40	-1592.5840	3265.1680	0.0000	1.0000
F81I	39	-1594.0333	3266.0666	0.0000	1.0000
K2PIG	38	-1595.3130	3266.6260	0.0000	1.0000
K2PI	37	-1596.9864	3267.9727	0.0000	1.0000
SYMG	41	-1594.2639	3270.5278	0.0000	1.0000
SYMIG	42	-1594.2474	3272.4947	0.0000	1.0000
SYMI	41	-1595.9740	3273.9479	0.0000	1.0000
F81	38	-1601.7793	3279.5586	0.0000	1.0000
K2P	36	-1606.1019	3284.2038	0.0000	1.0000
SYM	40	-1604.6613	3289.3226	0.0000	1.0000
JC69G	36	-1629.4119	3330.8238	0.0000	1.0000
JC69IG	37	-1629.4075	3332.8150	0.0000	1.0000
JC69I	36	-1630.7845	3333.5690	0.0000	1.0000
JC69	35	-1639.2656	3348.5313	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1549.9854	3343.2596	0.8428	0.8428
HKYI	40	-1551.9914	3347.2715	0.1134	0.9562
HKYIG	41	-1549.9891	3349.3492	0.0401	0.9963
GTRG	44	-1543.9278	3355.4733	0.0019	0.9982
HKY	39	-1559.3292	3355.8648	0.0015	0.9997
GTRI	44	-1546.3690	3360.3557	0.0002	0.9999
GTRIG	45	-1543.9303	3361.5605	0.0001	1.0000
GTR	43	-1553.4342	3368.4039	0.0000	1.0000
K2PG	37	-1595.3317	3415.7056	0.0000	1.0000
K2PI	37	-1596.9864	3419.0148	0.0000	1.0000
K2PIG	38	-1595.3130	3421.7503	0.0000	1.0000
F81G	39	-1592.5854	3422.3773	0.0000	1.0000
F81I	39	-1594.0333	3425.2731	0.0000	1.0000
F81IG	40	-1592.5840	3428.4568	0.0000	1.0000
K2P	36	-1606.1019	3431.1637	0.0000	1.0000
F81	38	-1601.7793	3434.6829	0.0000	1.0000
SYMG	41	-1594.2639	3437.8987	0.0000	1.0000
SYMI	41	-1595.9740	3441.3189	0.0000	1.0000
SYMIG	42	-1594.2474	3443.9479	0.0000	1.0000
SYM	40	-1604.6613	3452.6113	0.0000	1.0000
JC69G	36	-1629.4119	3477.7837	0.0000	1.0000
JC69I	36	-1630.7845	3480.5289	0.0000	1.0000
JC69IG	37	-1629.4075	3483.8571	0.0000	1.0000
JC69	35	-1639.2656	3491.4089	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/chr7_10870.phylip = 1 - 438;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10870.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/chr7_10870.phylip = 1 - 438;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10870.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/chr7_10870.phylip = 1 - 438;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10870.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

