
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:03 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_24707.phylip" (19 taxa, 275 characters)

Minimum AIC  model: GTRG
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	-989.5627	2073.1426	0.3429	0.3429
HKYI	40	-989.9404	2073.8979	0.2350	0.5779
GTRG	44	-984.6559	2074.5293	0.1714	0.7493
GTRI	44	-985.0348	2075.2870	0.1173	0.8667
HKYIG	41	-989.5289	2075.8389	0.0891	0.9557
GTRIG	45	-984.5813	2077.2413	0.0442	0.9999
K2PG	37	-1002.5858	2091.0365	0.0000	0.9999
K2PI	37	-1003.1546	2092.1741	0.0000	1.0000
HKY	39	-1000.9451	2093.1668	0.0000	1.0000
K2PIG	38	-1002.5684	2093.6962	0.0000	1.0000
GTR	43	-995.8692	2094.1194	0.0000	1.0000
SYMG	41	-999.0929	2094.9668	0.0000	1.0000
SYMI	41	-999.7330	2096.2470	0.0000	1.0000
SYMIG	42	-999.0664	2097.7017	0.0000	1.0000
F81G	39	-1003.7900	2098.8565	0.0000	1.0000
F81I	39	-1004.2647	2099.8059	0.0000	1.0000
F81IG	40	-1003.7710	2101.5591	0.0000	1.0000
JC69G	36	-1015.1525	2113.4983	0.0000	1.0000
K2P	36	-1015.2017	2113.5966	0.0000	1.0000
JC69I	36	-1015.7421	2114.6775	0.0000	1.0000
JC69IG	37	-1015.1337	2116.1324	0.0000	1.0000
SYM	40	-1011.7917	2117.6005	0.0000	1.0000
F81	38	-1015.7370	2120.0332	0.0000	1.0000
JC69	35	-1027.8546	2136.2532	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-984.6559	2057.3119	0.3430	0.3430
GTRI	44	-985.0348	2058.0696	0.2348	0.5778
HKYG	40	-989.5627	2059.1255	0.1385	0.7163
GTRIG	45	-984.5813	2059.1627	0.1360	0.8523
HKYI	40	-989.9404	2059.8808	0.0949	0.9473
HKYIG	41	-989.5289	2061.0578	0.0527	1.0000
GTR	43	-995.8692	2077.7384	0.0000	1.0000
K2PG	37	-1002.5858	2079.1716	0.0000	1.0000
HKY	39	-1000.9451	2079.8902	0.0000	1.0000
SYMG	41	-999.0929	2080.1857	0.0000	1.0000
K2PI	37	-1003.1546	2080.3092	0.0000	1.0000
K2PIG	38	-1002.5684	2081.1369	0.0000	1.0000
SYMI	41	-999.7330	2081.4659	0.0000	1.0000
SYMIG	42	-999.0664	2082.1327	0.0000	1.0000
F81G	39	-1003.7900	2085.5799	0.0000	1.0000
F81I	39	-1004.2647	2086.5293	0.0000	1.0000
F81IG	40	-1003.7710	2087.5420	0.0000	1.0000
JC69G	36	-1015.1525	2102.3050	0.0000	1.0000
K2P	36	-1015.2017	2102.4033	0.0000	1.0000
JC69I	36	-1015.7421	2103.4842	0.0000	1.0000
SYM	40	-1011.7917	2103.5834	0.0000	1.0000
JC69IG	37	-1015.1337	2104.2674	0.0000	1.0000
F81	38	-1015.7370	2107.4739	0.0000	1.0000
JC69	35	-1027.8546	2125.7092	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-989.5627	2203.7963	0.5657	0.5657
HKYI	40	-989.9404	2204.5516	0.3878	0.9535
HKYIG	41	-989.5289	2209.3454	0.0353	0.9888
K2PG	37	-1002.5858	2212.9921	0.0057	0.9945
K2PI	37	-1003.1546	2214.1297	0.0032	0.9978
GTRG	44	-984.6559	2216.4498	0.0010	0.9988
GTRI	44	-985.0348	2217.2076	0.0007	0.9995
K2PIG	38	-1002.5684	2218.5742	0.0003	0.9998
HKY	39	-1000.9451	2220.9443	0.0001	0.9999
GTRIG	45	-984.5813	2221.9174	0.0001	1.0000
F81G	39	-1003.7900	2226.6340	0.0000	1.0000
F81I	39	-1004.2647	2227.5834	0.0000	1.0000
SYMG	41	-999.0929	2228.4733	0.0000	1.0000
SYMI	41	-999.7330	2229.7535	0.0000	1.0000
F81IG	40	-1003.7710	2232.2128	0.0000	1.0000
JC69G	36	-1015.1525	2232.5088	0.0000	1.0000
K2P	36	-1015.2017	2232.6071	0.0000	1.0000
GTR	43	-995.8692	2233.2596	0.0000	1.0000
JC69I	36	-1015.7421	2233.6880	0.0000	1.0000
SYMIG	42	-999.0664	2234.0371	0.0000	1.0000
JC69IG	37	-1015.1337	2238.0880	0.0000	1.0000
F81	38	-1015.7370	2244.9112	0.0000	1.0000
SYM	40	-1011.7917	2248.2542	0.0000	1.0000
JC69	35	-1027.8546	2252.2962	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/chr2_24707.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24707.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24707.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24707.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/chr2_24707.phylip = 1 - 275;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24707.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

