
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:07 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/chr3_17991.phylip" (19 taxa, 338 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	-1524.8664	3140.7765	0.5507	0.5507
HKYG	40	-1525.4959	3142.0355	0.2934	0.8442
HKYIG	41	-1524.8717	3143.3786	0.1499	0.9941
GTRI	44	-1524.7347	3150.9847	0.0033	0.9974
GTRG	44	-1525.4185	3152.3524	0.0017	0.9991
GTRIG	45	-1524.7423	3153.6627	0.0009	1.0000
HKY	39	-1538.2206	3164.9110	0.0000	1.0000
K2PG	37	-1543.8998	3171.1730	0.0000	1.0000
K2PI	37	-1544.1979	3171.7691	0.0000	1.0000
K2PIG	38	-1543.8997	3173.7124	0.0000	1.0000
GTR	43	-1538.0510	3174.9727	0.0000	1.0000
SYMG	41	-1543.4697	3180.5746	0.0000	1.0000
SYMI	41	-1543.6062	3180.8475	0.0000	1.0000
SYMIG	42	-1543.3951	3183.0343	0.0000	1.0000
K2P	36	-1556.8643	3194.5791	0.0000	1.0000
SYM	40	-1557.1437	3205.3312	0.0000	1.0000
F81I	39	-1565.2911	3219.0520	0.0000	1.0000
F81G	39	-1565.6901	3219.8500	0.0000	1.0000
F81IG	40	-1565.2933	3221.6304	0.0000	1.0000
F81	38	-1577.4100	3240.7331	0.0000	1.0000
JC69G	36	-1580.9126	3242.6757	0.0000	1.0000
JC69I	36	-1581.5598	3243.9701	0.0000	1.0000
JC69IG	37	-1580.7027	3244.7787	0.0000	1.0000
JC69	35	-1593.4267	3265.1978	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1524.8664	3129.7327	0.5160	0.5160
HKYG	40	-1525.4959	3130.9917	0.2750	0.7910
HKYIG	41	-1524.8717	3131.7434	0.1888	0.9798
GTRI	44	-1524.7347	3137.4694	0.0108	0.9906
GTRG	44	-1525.4185	3138.8371	0.0054	0.9961
GTRIG	45	-1524.7423	3139.4846	0.0039	1.0000
HKY	39	-1538.2206	3154.4412	0.0000	1.0000
K2PG	37	-1543.8998	3161.7996	0.0000	1.0000
GTR	43	-1538.0510	3162.1019	0.0000	1.0000
K2PI	37	-1544.1979	3162.3957	0.0000	1.0000
K2PIG	38	-1543.8997	3163.7993	0.0000	1.0000
SYMG	41	-1543.4697	3168.9394	0.0000	1.0000
SYMI	41	-1543.6062	3169.2124	0.0000	1.0000
SYMIG	42	-1543.3951	3170.7902	0.0000	1.0000
K2P	36	-1556.8643	3185.7286	0.0000	1.0000
SYM	40	-1557.1437	3194.2874	0.0000	1.0000
F81I	39	-1565.2911	3208.5822	0.0000	1.0000
F81G	39	-1565.6901	3209.3802	0.0000	1.0000
F81IG	40	-1565.2933	3210.5867	0.0000	1.0000
F81	38	-1577.4100	3230.8201	0.0000	1.0000
JC69G	36	-1580.9126	3233.8252	0.0000	1.0000
JC69I	36	-1581.5598	3235.1196	0.0000	1.0000
JC69IG	37	-1580.7027	3235.4054	0.0000	1.0000
JC69	35	-1593.4267	3256.8534	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1524.8664	3282.6545	0.6301	0.6301
HKYG	40	-1525.4959	3283.9136	0.3357	0.9658
HKYIG	41	-1524.8717	3288.4883	0.0341	0.9999
K2PG	37	-1543.8998	3303.2523	0.0000	1.0000
HKY	39	-1538.2206	3303.5400	0.0000	1.0000
K2PI	37	-1544.1979	3303.8484	0.0000	1.0000
GTRI	44	-1524.7347	3305.6834	0.0000	1.0000
GTRG	44	-1525.4185	3307.0511	0.0000	1.0000
K2PIG	38	-1543.8997	3309.0751	0.0000	1.0000
GTRIG	45	-1524.7423	3311.5217	0.0000	1.0000
K2P	36	-1556.8643	3323.3583	0.0000	1.0000
SYMG	41	-1543.4697	3325.6843	0.0000	1.0000
SYMI	41	-1543.6062	3325.9573	0.0000	1.0000
GTR	43	-1538.0510	3326.4929	0.0000	1.0000
SYMIG	42	-1543.3951	3331.3582	0.0000	1.0000
SYM	40	-1557.1437	3347.2092	0.0000	1.0000
F81I	39	-1565.2911	3357.6809	0.0000	1.0000
F81G	39	-1565.6901	3358.4789	0.0000	1.0000
F81IG	40	-1565.2933	3363.5085	0.0000	1.0000
JC69G	36	-1580.9126	3371.4548	0.0000	1.0000
JC69I	36	-1581.5598	3372.7493	0.0000	1.0000
F81	38	-1577.4100	3376.0958	0.0000	1.0000
JC69IG	37	-1580.7027	3376.8581	0.0000	1.0000
JC69	35	-1593.4267	3390.6600	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/chr3_17991.phylip = 1 - 338;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17991.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/chr3_17991.phylip = 1 - 338;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17991.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/chr3_17991.phylip = 1 - 338;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17991.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

