
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:24 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_29841.phylip" (19 taxa, 345 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	-1611.6304	3324.4608	0.5401	0.5401
GTRIG	45	-1611.4074	3326.6610	0.1798	0.7199
SYMG	41	-1616.6709	3326.7082	0.1756	0.8955
SYMIG	42	-1616.4497	3328.8596	0.0599	0.9554
K2PG	37	-1623.2112	3329.5820	0.0417	0.9971
SYMI	41	-1621.6275	3336.6214	0.0012	0.9983
K2PIG	38	-1625.7515	3337.1894	0.0009	0.9993
GTRI	44	-1618.8472	3338.8944	0.0004	0.9996
HKYG	40	-1624.5247	3339.8388	0.0002	0.9999
HKYIG	41	-1624.2603	3341.8869	0.0001	1.0000
K2PI	37	-1631.2554	3345.6703	0.0000	1.0000
HKYI	40	-1629.5958	3349.9811	0.0000	1.0000
SYM	40	-1670.7097	3432.2088	0.0000	1.0000
K2P	36	-1678.0095	3436.6683	0.0000	1.0000
GTR	43	-1669.2630	3437.0974	0.0000	1.0000
HKY	39	-1676.3956	3441.0206	0.0000	1.0000
JC69G	36	-1688.2281	3457.1056	0.0000	1.0000
JC69IG	37	-1688.0117	3459.1830	0.0000	1.0000
F81G	39	-1687.3198	3462.8691	0.0000	1.0000
JC69I	36	-1692.0893	3464.8279	0.0000	1.0000
F81IG	40	-1687.1039	3464.9973	0.0000	1.0000
F81I	39	-1691.0554	3470.3404	0.0000	1.0000
JC69	35	-1738.9124	3555.9801	0.0000	1.0000
F81	38	-1737.9096	3561.5054	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1611.6304	3311.2608	0.6018	0.6018
GTRIG	45	-1611.4074	3312.8148	0.2767	0.8784
SYMG	41	-1616.6709	3315.3419	0.0782	0.9566
SYMIG	42	-1616.4497	3316.8993	0.0359	0.9925
K2PG	37	-1623.2112	3320.4224	0.0062	0.9987
SYMI	41	-1621.6275	3325.2551	0.0006	0.9993
GTRI	44	-1618.8472	3325.6944	0.0004	0.9997
K2PIG	38	-1625.7515	3327.5031	0.0002	0.9999
HKYG	40	-1624.5247	3329.0494	0.0001	1.0000
HKYIG	41	-1624.2603	3330.5205	0.0000	1.0000
K2PI	37	-1631.2554	3336.5107	0.0000	1.0000
HKYI	40	-1629.5958	3339.1916	0.0000	1.0000
SYM	40	-1670.7097	3421.4194	0.0000	1.0000
GTR	43	-1669.2630	3424.5260	0.0000	1.0000
K2P	36	-1678.0095	3428.0189	0.0000	1.0000
HKY	39	-1676.3956	3430.7911	0.0000	1.0000
JC69G	36	-1688.2281	3448.4562	0.0000	1.0000
JC69IG	37	-1688.0117	3450.0234	0.0000	1.0000
F81G	39	-1687.3198	3452.6396	0.0000	1.0000
F81IG	40	-1687.1039	3454.2078	0.0000	1.0000
JC69I	36	-1692.0893	3456.1785	0.0000	1.0000
F81I	39	-1691.0554	3460.1109	0.0000	1.0000
JC69	35	-1738.9124	3547.8247	0.0000	1.0000
F81	38	-1737.9096	3551.8192	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1623.2112	3462.6335	0.9891	0.9891
SYMG	41	-1616.6709	3472.9272	0.0058	0.9949
K2PIG	38	-1625.7515	3473.5578	0.0042	0.9991
SYMIG	42	-1616.4497	3478.3282	0.0004	0.9994
K2PI	37	-1631.2554	3478.7219	0.0003	0.9998
GTRG	44	-1611.6304	3480.3768	0.0001	0.9999
HKYG	40	-1624.5247	3482.7911	0.0000	0.9999
SYMI	41	-1621.6275	3482.8404	0.0000	1.0000
GTRIG	45	-1611.4074	3485.7743	0.0000	1.0000
HKYIG	41	-1624.2603	3488.1058	0.0000	1.0000
HKYI	40	-1629.5958	3492.9334	0.0000	1.0000
GTRI	44	-1618.8472	3494.8103	0.0000	1.0000
K2P	36	-1678.0095	3566.3865	0.0000	1.0000
SYM	40	-1670.7097	3575.1611	0.0000	1.0000
HKY	39	-1676.3956	3580.6894	0.0000	1.0000
JC69G	36	-1688.2281	3586.8238	0.0000	1.0000
GTR	43	-1669.2630	3589.7984	0.0000	1.0000
JC69IG	37	-1688.0117	3592.2345	0.0000	1.0000
JC69I	36	-1692.0893	3594.5461	0.0000	1.0000
F81G	39	-1687.3198	3602.5378	0.0000	1.0000
F81IG	40	-1687.1039	3607.9496	0.0000	1.0000
F81I	39	-1691.0554	3610.0091	0.0000	1.0000
JC69	35	-1738.9124	3682.3488	0.0000	1.0000
F81	38	-1737.9096	3697.8738	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/chr1_29841.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29841.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/chr1_29841.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29841.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/chr1_29841.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29841.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

