
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:36 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_11783.phylip" (19 taxa, 366 characters)

Minimum AIC  model: HKYI
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	-1064.8464	2219.7850	0.4014	0.4014
HKYG	40	-1064.8673	2219.8270	0.3931	0.7945
HKYIG	41	-1064.7704	2222.1705	0.1218	0.9162
GTRI	44	-1062.1826	2224.7016	0.0344	0.9506
GTRG	44	-1062.1930	2224.7225	0.0340	0.9846
GTRIG	45	-1062.1094	2227.1562	0.0101	0.9947
HKY	39	-1070.5110	2228.5925	0.0049	0.9996
GTR	43	-1067.8573	2233.4663	0.0004	1.0000
F81I	39	-1089.9014	2267.3734	0.0000	1.0000
F81G	39	-1090.0400	2267.6505	0.0000	1.0000
F81IG	40	-1089.8869	2269.8662	0.0000	1.0000
F81	38	-1095.7103	2276.4847	0.0000	1.0000
SYMI	41	-1111.0577	2314.7451	0.0000	1.0000
K2PI	37	-1116.0876	2314.7484	0.0000	1.0000
K2PG	37	-1116.2852	2315.1437	0.0000	1.0000
SYMG	41	-1111.3909	2315.4114	0.0000	1.0000
SYMIG	42	-1111.0593	2317.3013	0.0000	1.0000
K2PIG	38	-1119.4587	2323.9816	0.0000	1.0000
K2P	36	-1123.4885	2327.0743	0.0000	1.0000
SYM	40	-1119.4019	2328.8961	0.0000	1.0000
JC69I	36	-1137.1630	2354.4232	0.0000	1.0000
JC69G	36	-1137.3788	2354.8548	0.0000	1.0000
JC69IG	37	-1137.1600	2356.8932	0.0000	1.0000
JC69	35	-1143.8863	2365.4089	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1064.8464	2209.6927	0.3317	0.3317
HKYG	40	-1064.8673	2209.7347	0.3248	0.6565
HKYIG	41	-1064.7704	2211.5409	0.1316	0.7881
GTRI	44	-1062.1826	2212.3651	0.0872	0.8753
GTRG	44	-1062.1930	2212.3860	0.0863	0.9616
GTRIG	45	-1062.1094	2214.2187	0.0345	0.9961
HKY	39	-1070.5110	2219.0219	0.0031	0.9992
GTR	43	-1067.8573	2221.7147	0.0008	1.0000
F81I	39	-1089.9014	2257.8028	0.0000	1.0000
F81G	39	-1090.0400	2258.0799	0.0000	1.0000
F81IG	40	-1089.8869	2259.7739	0.0000	1.0000
F81	38	-1095.7103	2267.4205	0.0000	1.0000
SYMI	41	-1111.0577	2304.1155	0.0000	1.0000
SYMG	41	-1111.3909	2304.7818	0.0000	1.0000
SYMIG	42	-1111.0593	2306.1187	0.0000	1.0000
K2PI	37	-1116.0876	2306.1752	0.0000	1.0000
K2PG	37	-1116.2852	2306.5705	0.0000	1.0000
K2PIG	38	-1119.4587	2314.9174	0.0000	1.0000
SYM	40	-1119.4019	2318.8038	0.0000	1.0000
K2P	36	-1123.4885	2318.9770	0.0000	1.0000
JC69I	36	-1137.1630	2346.3260	0.0000	1.0000
JC69G	36	-1137.3788	2346.7576	0.0000	1.0000
JC69IG	37	-1137.1600	2348.3201	0.0000	1.0000
JC69	35	-1143.8863	2357.7726	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1064.8464	2365.7980	0.4757	0.4757
HKYG	40	-1064.8673	2365.8400	0.4658	0.9415
HKY	39	-1070.5110	2371.2246	0.0315	0.9731
HKYIG	41	-1064.7704	2371.5488	0.0268	0.9999
GTRI	44	-1062.1826	2384.0810	0.0001	0.9999
GTRG	44	-1062.1930	2384.1019	0.0001	1.0000
GTR	43	-1067.8573	2389.5279	0.0000	1.0000
GTRIG	45	-1062.1094	2389.8372	0.0000	1.0000
F81I	39	-1089.9014	2410.0055	0.0000	1.0000
F81G	39	-1090.0400	2410.2826	0.0000	1.0000
F81	38	-1095.7103	2415.7206	0.0000	1.0000
F81IG	40	-1089.8869	2415.8792	0.0000	1.0000
K2PI	37	-1116.0876	2450.5726	0.0000	1.0000
K2PG	37	-1116.2852	2450.9679	0.0000	1.0000
K2P	36	-1123.4885	2459.4718	0.0000	1.0000
K2PIG	38	-1119.4587	2463.2175	0.0000	1.0000
SYMI	41	-1111.0577	2464.1234	0.0000	1.0000
SYMG	41	-1111.3909	2464.7898	0.0000	1.0000
SYMIG	42	-1111.0593	2470.0293	0.0000	1.0000
SYM	40	-1119.4019	2474.9091	0.0000	1.0000
JC69I	36	-1137.1630	2486.8208	0.0000	1.0000
JC69G	36	-1137.3788	2487.2524	0.0000	1.0000
JC69IG	37	-1137.1600	2492.7175	0.0000	1.0000
JC69	35	-1143.8863	2494.3647	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11783.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11783.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 AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11783.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11783.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/chr5_11783.phylip = 1 - 366;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11783.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

