
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:41 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/chr5_3302.phylip" (19 taxa, 294 characters)

Minimum AIC  model: SYMIG
Minimum AICc model: K2PIG
Minimum BIC  model: K2PIG


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
K2PIG	38	-1074.7385	2237.1004	0.5677	0.5677
SYMIG	42	-1070.3975	2239.1855	0.2001	0.7678
HKYIG	41	-1072.0804	2239.8275	0.1452	0.9130
HKYG	40	-1075.0484	2243.0612	0.0288	0.9418
K2PG	37	-1079.5464	2244.0772	0.0173	0.9591
GTRIG	45	-1068.8626	2244.4188	0.0146	0.9738
SYMG	41	-1074.7252	2245.1171	0.0103	0.9841
K2PI	37	-1080.2205	2245.4255	0.0088	0.9929
GTRG	44	-1071.7755	2247.4546	0.0032	0.9961
SYMI	41	-1076.3255	2248.3176	0.0021	0.9982
HKYI	40	-1077.8956	2248.7556	0.0017	0.9999
GTRI	44	-1074.9061	2253.7159	0.0001	1.0000
JC69IG	37	-1106.9576	2298.8996	0.0000	1.0000
JC69G	36	-1110.0329	2302.4316	0.0000	1.0000
F81IG	40	-1105.2177	2303.3999	0.0000	1.0000
F81G	39	-1108.6027	2307.4888	0.0000	1.0000
JC69I	36	-1112.7667	2307.8992	0.0000	1.0000
F81I	39	-1110.5906	2311.4647	0.0000	1.0000
HKY	39	-1124.4595	2339.2024	0.0000	1.0000
SYM	40	-1123.5567	2340.0779	0.0000	1.0000
K2P	36	-1128.9029	2340.1715	0.0000	1.0000
GTR	43	-1123.0179	2347.1718	0.0000	1.0000
JC69	35	-1156.4726	2392.7126	0.0000	1.0000
F81	38	-1155.4909	2398.6054	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMIG	42	-1070.3975	2224.7950	0.3810	0.3810
K2PIG	38	-1074.7385	2225.4769	0.2709	0.6520
HKYIG	41	-1072.0804	2226.1608	0.1925	0.8444
GTRIG	45	-1068.8626	2227.7253	0.0880	0.9325
HKYG	40	-1075.0484	2230.0967	0.0269	0.9594
SYMG	41	-1074.7252	2231.4504	0.0137	0.9730
GTRG	44	-1071.7755	2231.5510	0.0130	0.9860
K2PG	37	-1079.5464	2233.0929	0.0060	0.9920
K2PI	37	-1080.2205	2234.4411	0.0031	0.9951
SYMI	41	-1076.3255	2234.6509	0.0028	0.9979
HKYI	40	-1077.8956	2235.7912	0.0016	0.9994
GTRI	44	-1074.9061	2237.8123	0.0006	1.0000
JC69IG	37	-1106.9576	2287.9153	0.0000	1.0000
F81IG	40	-1105.2177	2290.4355	0.0000	1.0000
JC69G	36	-1110.0329	2292.0658	0.0000	1.0000
F81G	39	-1108.6027	2295.2053	0.0000	1.0000
JC69I	36	-1112.7667	2297.5335	0.0000	1.0000
F81I	39	-1110.5906	2299.1813	0.0000	1.0000
HKY	39	-1124.4595	2326.9189	0.0000	1.0000
SYM	40	-1123.5567	2327.1135	0.0000	1.0000
K2P	36	-1128.9029	2329.8058	0.0000	1.0000
GTR	43	-1123.0179	2332.0358	0.0000	1.0000
JC69	35	-1156.4726	2382.9451	0.0000	1.0000
F81	38	-1155.4909	2386.9819	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PIG	38	-1074.7385	2365.4529	0.8211	0.8211
K2PG	37	-1079.5464	2369.3853	0.1149	0.9360
K2PI	37	-1080.2205	2370.7335	0.0586	0.9946
HKYIG	41	-1072.0804	2377.1876	0.0023	0.9969
HKYG	40	-1075.0484	2377.4399	0.0020	0.9990
SYMIG	42	-1070.3975	2379.5054	0.0007	0.9997
SYMG	41	-1074.7252	2382.4772	0.0002	0.9998
HKYI	40	-1077.8956	2383.1344	0.0001	1.0000
SYMI	41	-1076.3255	2385.6777	0.0000	1.0000
GTRIG	45	-1068.8626	2393.4864	0.0000	1.0000
GTRG	44	-1071.7755	2393.6285	0.0000	1.0000
GTRI	44	-1074.9061	2399.8898	0.0000	1.0000
JC69IG	37	-1106.9576	2424.2077	0.0000	1.0000
JC69G	36	-1110.0329	2424.6747	0.0000	1.0000
JC69I	36	-1112.7667	2430.1424	0.0000	1.0000
F81IG	40	-1105.2177	2437.7787	0.0000	1.0000
F81G	39	-1108.6027	2438.8649	0.0000	1.0000
F81I	39	-1110.5906	2442.8409	0.0000	1.0000
K2P	36	-1128.9029	2462.4146	0.0000	1.0000
HKY	39	-1124.4595	2470.5785	0.0000	1.0000
SYM	40	-1123.5567	2474.4567	0.0000	1.0000
GTR	43	-1123.0179	2490.4297	0.0000	1.0000
JC69	35	-1156.4726	2511.8704	0.0000	1.0000
F81	38	-1155.4909	2526.9579	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.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=Fixed(Equal) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3302.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

