
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:57 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/chr2_13064.phylip" (19 taxa, 398 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: SYMG


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
SYMG	41	-1788.8181	3669.3103	0.4951	0.4951
SYMIG	42	-1788.2486	3670.6717	0.2507	0.7458
GTRG	44	-1786.1157	3671.4496	0.1699	0.9157
GTRIG	45	-1785.5482	3672.8578	0.0840	0.9997
SYMI	41	-1796.6684	3685.0111	0.0002	0.9999
GTRI	44	-1794.3728	3687.9638	0.0000	1.0000
K2PG	37	-1804.4289	3690.6689	0.0000	1.0000
K2PIG	38	-1803.8039	3691.8640	0.0000	1.0000
HKYG	40	-1802.9223	3695.0322	0.0000	1.0000
HKYIG	41	-1802.3476	3696.3694	0.0000	1.0000
K2PI	37	-1812.6046	3707.0202	0.0000	1.0000
HKYI	40	-1811.3301	3711.8480	0.0000	1.0000
JC69G	36	-1843.8472	3767.0739	0.0000	1.0000
SYM	40	-1839.1889	3767.5654	0.0000	1.0000
JC69IG	37	-1843.3826	3768.5764	0.0000	1.0000
F81G	39	-1842.0113	3770.7376	0.0000	1.0000
GTR	43	-1837.6080	3771.9053	0.0000	1.0000
F81IG	40	-1841.5379	3772.2635	0.0000	1.0000
JC69I	36	-1851.5506	3782.4807	0.0000	1.0000
F81I	39	-1849.8456	3786.4062	0.0000	1.0000
K2P	36	-1853.9864	3787.3524	0.0000	1.0000
HKY	39	-1852.7296	3792.1743	0.0000	1.0000
JC69	35	-1891.8912	3860.7438	0.0000	1.0000
F81	38	-1890.2310	3864.7183	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-1788.8181	3659.6362	0.3478	0.3478
GTRG	44	-1786.1157	3660.2315	0.2583	0.6061
SYMIG	42	-1788.2486	3660.4971	0.2261	0.8322
GTRIG	45	-1785.5482	3661.0964	0.1676	0.9998
SYMI	41	-1796.6684	3675.3369	0.0001	0.9999
GTRI	44	-1794.3728	3676.7457	0.0001	1.0000
K2PG	37	-1804.4289	3682.8578	0.0000	1.0000
K2PIG	38	-1803.8039	3683.6078	0.0000	1.0000
HKYG	40	-1802.9223	3685.8445	0.0000	1.0000
HKYIG	41	-1802.3476	3686.6952	0.0000	1.0000
K2PI	37	-1812.6046	3699.2091	0.0000	1.0000
HKYI	40	-1811.3301	3702.6603	0.0000	1.0000
SYM	40	-1839.1889	3758.3778	0.0000	1.0000
JC69G	36	-1843.8472	3759.6944	0.0000	1.0000
JC69IG	37	-1843.3826	3760.7653	0.0000	1.0000
GTR	43	-1837.6080	3761.2161	0.0000	1.0000
F81G	39	-1842.0113	3762.0225	0.0000	1.0000
F81IG	40	-1841.5379	3763.0758	0.0000	1.0000
JC69I	36	-1851.5506	3775.1012	0.0000	1.0000
F81I	39	-1849.8456	3777.6912	0.0000	1.0000
K2P	36	-1853.9864	3779.9729	0.0000	1.0000
HKY	39	-1852.7296	3783.4592	0.0000	1.0000
JC69	35	-1891.8912	3853.7825	0.0000	1.0000
F81	38	-1890.2310	3856.4620	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-1788.8181	3823.0807	0.8930	0.8930
SYMIG	42	-1788.2486	3827.9281	0.0791	0.9721
K2PG	37	-1804.4289	3830.3565	0.0235	0.9956
K2PIG	38	-1803.8039	3835.0930	0.0022	0.9978
GTRG	44	-1786.1157	3835.6354	0.0017	0.9995
SYMI	41	-1796.6684	3838.7814	0.0003	0.9998
GTRIG	45	-1785.5482	3840.4868	0.0001	1.0000
HKYG	40	-1802.9223	3845.3026	0.0000	1.0000
K2PI	37	-1812.6046	3846.7078	0.0000	1.0000
HKYIG	41	-1802.3476	3850.1397	0.0000	1.0000
GTRI	44	-1794.3728	3852.1496	0.0000	1.0000
HKYI	40	-1811.3301	3862.1184	0.0000	1.0000
JC69G	36	-1843.8472	3903.2066	0.0000	1.0000
JC69IG	37	-1843.3826	3908.2640	0.0000	1.0000
F81G	39	-1842.0113	3917.4941	0.0000	1.0000
SYM	40	-1839.1889	3917.8358	0.0000	1.0000
JC69I	36	-1851.5506	3918.6135	0.0000	1.0000
F81IG	40	-1841.5379	3922.5339	0.0000	1.0000
K2P	36	-1853.9864	3923.4852	0.0000	1.0000
GTR	43	-1837.6080	3932.6335	0.0000	1.0000
F81I	39	-1849.8456	3933.1628	0.0000	1.0000
HKY	39	-1852.7296	3938.9308	0.0000	1.0000
JC69	35	-1891.8912	3993.3083	0.0000	1.0000
F81	38	-1890.2310	4007.9472	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.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=Fixed(Equal);
END;


[Mrbayes block for the best AICc model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13064.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=Fixed(Equal);
END;


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End of Output

