
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:03 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/chr19_2440.phylip" (19 taxa, 393 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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
GTRG	44	-1152.6169	2404.6131	0.4951	0.4951
GTRIG	45	-1151.8060	2405.5428	0.3110	0.8061
GTRI	44	-1154.4348	2408.2488	0.0804	0.8865
SYMG	41	-1158.6404	2409.0927	0.0527	0.9392
SYMIG	42	-1157.7095	2409.7389	0.0382	0.9773
SYMI	41	-1160.0730	2411.9580	0.0126	0.9899
K2PG	37	-1166.6171	2415.1553	0.0025	0.9925
K2PIG	38	-1165.5244	2415.4217	0.0022	0.9947
HKYG	40	-1163.1250	2415.5681	0.0021	0.9967
HKYIG	41	-1162.1025	2416.0169	0.0017	0.9984
K2PI	37	-1167.6176	2417.1563	0.0009	0.9993
HKYI	40	-1164.2621	2417.8424	0.0007	1.0000
GTR	43	-1178.2255	2453.2935	0.0000	1.0000
SYM	40	-1186.4561	2462.2303	0.0000	1.0000
JC69G	36	-1193.6751	2466.8334	0.0000	1.0000
F81G	39	-1190.0811	2467.0008	0.0000	1.0000
JC69IG	37	-1192.8228	2467.5666	0.0000	1.0000
F81IG	40	-1189.2765	2467.8712	0.0000	1.0000
JC69I	36	-1194.6853	2468.8538	0.0000	1.0000
F81I	39	-1191.1471	2469.1327	0.0000	1.0000
HKY	39	-1191.3891	2469.6168	0.0000	1.0000
K2P	36	-1196.7189	2472.9209	0.0000	1.0000
F81	38	-1217.3941	2519.1611	0.0000	1.0000
JC69	35	-1221.9411	2520.9411	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1152.6169	2393.2338	0.4759	0.4759
GTRIG	45	-1151.8060	2393.6120	0.3939	0.8697
GTRI	44	-1154.4348	2396.8695	0.0773	0.9470
SYMG	41	-1158.6404	2399.2808	0.0231	0.9701
SYMIG	42	-1157.7095	2399.4189	0.0216	0.9917
SYMI	41	-1160.0730	2402.1460	0.0055	0.9973
HKYIG	41	-1162.1025	2406.2049	0.0007	0.9980
HKYG	40	-1163.1250	2406.2499	0.0007	0.9987
K2PIG	38	-1165.5244	2407.0488	0.0005	0.9992
K2PG	37	-1166.6171	2407.2342	0.0004	0.9996
HKYI	40	-1164.2621	2408.5242	0.0002	0.9998
K2PI	37	-1167.6176	2409.2352	0.0002	1.0000
GTR	43	-1178.2255	2442.4511	0.0000	1.0000
SYM	40	-1186.4561	2452.9121	0.0000	1.0000
F81G	39	-1190.0811	2458.1622	0.0000	1.0000
F81IG	40	-1189.2765	2458.5530	0.0000	1.0000
JC69G	36	-1193.6751	2459.3503	0.0000	1.0000
JC69IG	37	-1192.8228	2459.6455	0.0000	1.0000
F81I	39	-1191.1471	2460.2941	0.0000	1.0000
HKY	39	-1191.3891	2460.7783	0.0000	1.0000
JC69I	36	-1194.6853	2461.3706	0.0000	1.0000
K2P	36	-1196.7189	2465.4377	0.0000	1.0000
F81	38	-1217.3941	2510.7882	0.0000	1.0000
JC69	35	-1221.9411	2513.8822	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1166.6171	2554.2651	0.6446	0.6446
K2PI	37	-1167.6176	2556.2662	0.2370	0.8816
K2PIG	38	-1165.5244	2558.0536	0.0970	0.9786
SYMG	41	-1158.6404	2562.2070	0.0122	0.9907
SYMI	41	-1160.0730	2565.0722	0.0029	0.9937
HKYG	40	-1163.1250	2565.2023	0.0027	0.9964
SYMIG	42	-1157.7095	2566.3189	0.0016	0.9979
HKYI	40	-1164.2621	2567.4766	0.0009	0.9988
GTRG	44	-1152.6169	2568.0814	0.0006	0.9994
HKYIG	41	-1162.1025	2569.1311	0.0004	0.9998
GTRI	44	-1154.4348	2571.7171	0.0001	0.9999
GTRIG	45	-1151.8060	2572.4334	0.0001	1.0000
JC69G	36	-1193.6751	2602.4074	0.0000	1.0000
JC69I	36	-1194.6853	2604.4278	0.0000	1.0000
JC69IG	37	-1192.8228	2606.6765	0.0000	1.0000
K2P	36	-1196.7189	2608.4949	0.0000	1.0000
SYM	40	-1186.4561	2611.8645	0.0000	1.0000
F81G	39	-1190.0811	2613.1408	0.0000	1.0000
GTR	43	-1178.2255	2613.3249	0.0000	1.0000
F81I	39	-1191.1471	2615.2727	0.0000	1.0000
HKY	39	-1191.3891	2615.7568	0.0000	1.0000
F81IG	40	-1189.2765	2617.5054	0.0000	1.0000
JC69	35	-1221.9411	2652.9656	0.0000	1.0000
F81	38	-1217.3941	2661.7930	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/chr19_2440.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2440.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2440.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2440.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 BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2440.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2440.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

