
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:42 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_10530.phylip" (19 taxa, 339 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-841.9057	1774.8182	0.4628	0.4628
HKYI	40	-842.1062	1775.2190	0.3788	0.8416
HKYIG	41	-841.8272	1777.2503	0.1372	0.9788
HKY	39	-846.7198	1781.8745	0.0136	0.9924
GTRG	44	-841.7491	1784.9677	0.0029	0.9953
GTRI	44	-841.9615	1785.3923	0.0023	0.9976
GTRIG	45	-841.6661	1787.4619	0.0008	0.9985
K2PG	37	-852.2882	1787.9187	0.0007	0.9991
K2PI	37	-852.4612	1788.2645	0.0006	0.9997
K2PIG	38	-852.2247	1790.3295	0.0002	0.9999
GTR	43	-846.5762	1791.9795	0.0001	1.0000
K2P	36	-857.1653	1795.1517	0.0000	1.0000
SYMG	41	-851.6949	1796.9858	0.0000	1.0000
SYMI	41	-851.8477	1797.2913	0.0000	1.0000
SYMIG	42	-851.6273	1799.4574	0.0000	1.0000
SYM	40	-856.5608	1804.1284	0.0000	1.0000
F81G	39	-868.1715	1824.7778	0.0000	1.0000
F81I	39	-868.3613	1825.1574	0.0000	1.0000
F81IG	40	-868.1131	1827.2330	0.0000	1.0000
F81	38	-872.9129	1831.7058	0.0000	1.0000
JC69G	36	-878.2500	1837.3212	0.0000	1.0000
JC69I	36	-878.4089	1837.6391	0.0000	1.0000
JC69IG	37	-878.1968	1839.7358	0.0000	1.0000
JC69	35	-882.9510	1844.2189	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-841.9057	1763.8114	0.4371	0.4371
HKYI	40	-842.1062	1764.2123	0.3577	0.7949
HKYIG	41	-841.8272	1765.6544	0.1740	0.9688
HKY	39	-846.7198	1771.4397	0.0096	0.9785
GTRG	44	-841.7491	1771.4983	0.0094	0.9878
GTRI	44	-841.9615	1771.9230	0.0076	0.9954
GTRIG	45	-841.6661	1773.3322	0.0037	0.9992
K2PG	37	-852.2882	1778.5765	0.0003	0.9994
K2PI	37	-852.4612	1778.9223	0.0002	0.9997
GTR	43	-846.5762	1779.1524	0.0002	0.9999
K2PIG	38	-852.2247	1780.4495	0.0001	1.0000
SYMG	41	-851.6949	1785.3899	0.0000	1.0000
SYMI	41	-851.8477	1785.6953	0.0000	1.0000
K2P	36	-857.1653	1786.3305	0.0000	1.0000
SYMIG	42	-851.6273	1787.2547	0.0000	1.0000
SYM	40	-856.5608	1793.1217	0.0000	1.0000
F81G	39	-868.1715	1814.3430	0.0000	1.0000
F81I	39	-868.3613	1814.7226	0.0000	1.0000
F81IG	40	-868.1131	1816.2263	0.0000	1.0000
F81	38	-872.9129	1821.8258	0.0000	1.0000
JC69G	36	-878.2500	1828.5000	0.0000	1.0000
JC69I	36	-878.4089	1828.8179	0.0000	1.0000
JC69IG	37	-878.1968	1830.3936	0.0000	1.0000
JC69	35	-882.9510	1835.9020	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-841.9057	1916.8514	0.4131	0.4131
HKYI	40	-842.1062	1917.2523	0.3381	0.7512
K2PG	37	-852.2882	1920.1385	0.0799	0.8310
K2PI	37	-852.4612	1920.4843	0.0672	0.8982
HKY	39	-846.7198	1920.6537	0.0617	0.9599
HKYIG	41	-841.8272	1922.5204	0.0243	0.9842
K2P	36	-857.1653	1924.0665	0.0112	0.9954
K2PIG	38	-852.2247	1925.8375	0.0046	1.0000
GTRG	44	-841.7491	1939.8423	0.0000	1.0000
GTRI	44	-841.9615	1940.2670	0.0000	1.0000
SYMG	41	-851.6949	1942.2559	0.0000	1.0000
SYMI	41	-851.8477	1942.5613	0.0000	1.0000
GTR	43	-846.5762	1943.6704	0.0000	1.0000
GTRIG	45	-841.6661	1945.5022	0.0000	1.0000
SYM	40	-856.5608	1946.1617	0.0000	1.0000
SYMIG	42	-851.6273	1947.9467	0.0000	1.0000
F81G	39	-868.1715	1963.5570	0.0000	1.0000
F81I	39	-868.3613	1963.9366	0.0000	1.0000
JC69G	36	-878.2500	1966.2360	0.0000	1.0000
JC69I	36	-878.4089	1966.5539	0.0000	1.0000
F81	38	-872.9129	1967.2138	0.0000	1.0000
F81IG	40	-868.1131	1969.2663	0.0000	1.0000
JC69	35	-882.9510	1969.8120	0.0000	1.0000
JC69IG	37	-878.1968	1971.9556	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10530.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10530.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10530.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10530.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;


[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_10530.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10530.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

