
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:16 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/chr4_11305.phylip" (19 taxa, 301 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-840.9482	1774.5118	0.2652	0.2652
HKYG	40	-841.2442	1775.1037	0.1972	0.4624
GTRI	44	-835.8303	1775.1294	0.1947	0.6571
GTRIG	45	-834.5014	1775.2381	0.1844	0.8416
HKYIG	41	-840.5723	1776.4418	0.1010	0.9426
GTRG	44	-837.0520	1777.5727	0.0574	1.0000
F81G	39	-853.4403	1796.8347	0.0000	1.0000
F81IG	40	-853.0320	1798.6794	0.0000	1.0000
F81I	39	-854.6029	1799.1599	0.0000	1.0000
HKY	39	-857.1179	1804.1898	0.0000	1.0000
GTR	43	-852.9786	1806.6809	0.0000	1.0000
SYMI	41	-858.6334	1812.5640	0.0000	1.0000
K2PG	37	-864.4964	1813.6848	0.0000	1.0000
SYMG	41	-859.4699	1814.2371	0.0000	1.0000
K2PIG	38	-864.0199	1815.3527	0.0000	1.0000
K2PI	37	-865.5217	1815.7355	0.0000	1.0000
SYMIG	42	-859.0367	1816.0733	0.0000	1.0000
F81	38	-866.7651	1820.8432	0.0000	1.0000
JC69G	36	-874.8850	1831.8609	0.0000	1.0000
JC69IG	37	-874.5127	1833.7174	0.0000	1.0000
JC69I	36	-875.9345	1833.9598	0.0000	1.0000
K2P	36	-880.1056	1842.3021	0.0000	1.0000
SYM	40	-875.8902	1844.3958	0.0000	1.0000
JC69	35	-888.2572	1856.0239	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-834.5014	1759.0028	0.4051	0.4051
GTRI	44	-835.8303	1759.6606	0.2916	0.6967
HKYI	40	-840.9482	1761.8965	0.0953	0.7921
GTRG	44	-837.0520	1762.1039	0.0859	0.8780
HKYG	40	-841.2442	1762.4883	0.0709	0.9489
HKYIG	41	-840.5723	1763.1445	0.0511	1.0000
F81G	39	-853.4403	1784.8806	0.0000	1.0000
F81IG	40	-853.0320	1786.0640	0.0000	1.0000
F81I	39	-854.6029	1787.2059	0.0000	1.0000
GTR	43	-852.9786	1791.9571	0.0000	1.0000
HKY	39	-857.1179	1792.2358	0.0000	1.0000
SYMI	41	-858.6334	1799.2667	0.0000	1.0000
SYMG	41	-859.4699	1800.9398	0.0000	1.0000
SYMIG	42	-859.0367	1802.0733	0.0000	1.0000
K2PG	37	-864.4964	1802.9928	0.0000	1.0000
K2PIG	38	-864.0199	1804.0398	0.0000	1.0000
K2PI	37	-865.5217	1805.0435	0.0000	1.0000
F81	38	-866.7651	1809.5302	0.0000	1.0000
JC69G	36	-874.8850	1821.7700	0.0000	1.0000
JC69IG	37	-874.5127	1823.0254	0.0000	1.0000
JC69I	36	-875.9345	1823.8689	0.0000	1.0000
SYM	40	-875.8902	1831.7804	0.0000	1.0000
K2P	36	-880.1056	1832.2112	0.0000	1.0000
JC69	35	-888.2572	1846.5145	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-840.9482	1910.1809	0.5463	0.5463
HKYG	40	-841.2442	1910.7728	0.4063	0.9526
HKYIG	41	-840.5723	1915.1360	0.0459	0.9984
GTRI	44	-835.8303	1922.7735	0.0010	0.9994
GTRG	44	-837.0520	1925.2168	0.0003	0.9997
GTRIG	45	-834.5014	1925.8227	0.0002	0.9999
F81G	39	-853.4403	1929.4579	0.0000	1.0000
F81I	39	-854.6029	1931.7832	0.0000	1.0000
F81IG	40	-853.0320	1934.3485	0.0000	1.0000
HKY	39	-857.1179	1936.8131	0.0000	1.0000
K2PG	37	-864.4964	1940.1558	0.0000	1.0000
K2PI	37	-865.5217	1942.2066	0.0000	1.0000
K2PIG	38	-864.0199	1944.9100	0.0000	1.0000
F81	38	-866.7651	1950.4004	0.0000	1.0000
SYMI	41	-858.6334	1951.2583	0.0000	1.0000
GTR	43	-852.9786	1951.3629	0.0000	1.0000
SYMG	41	-859.4699	1952.9313	0.0000	1.0000
JC69G	36	-874.8850	1955.2260	0.0000	1.0000
JC69I	36	-875.9345	1957.3249	0.0000	1.0000
SYMIG	42	-859.0367	1957.7720	0.0000	1.0000
JC69IG	37	-874.5127	1960.1885	0.0000	1.0000
K2P	36	-880.1056	1965.6671	0.0000	1.0000
JC69	35	-888.2572	1976.2633	0.0000	1.0000
SYM	40	-875.8902	1980.0648	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11305.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

