
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:39 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/chr1_9442.phylip" (19 taxa, 747 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
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
SYMG	41	-3084.5876	6256.0603	0.6374	0.6374
SYMIG	42	-3084.1901	6257.5109	0.3086	0.9460
GTRG	44	-3084.2609	6262.1629	0.0301	0.9761
GTRIG	45	-3083.8586	6263.6230	0.0145	0.9906
K2PG	37	-3093.7214	6265.4089	0.0059	0.9966
K2PIG	38	-3093.3316	6266.8496	0.0029	0.9995
HKYG	40	-3093.2539	6271.1536	0.0003	0.9998
HKYIG	41	-3092.8519	6272.5889	0.0002	1.0000
SYMI	41	-3094.9214	6276.7279	0.0000	1.0000
GTRI	44	-3094.6499	6282.9408	0.0000	1.0000
K2PI	37	-3103.7560	6285.4781	0.0000	1.0000
HKYI	40	-3103.3705	6291.3870	0.0000	1.0000
JC69G	36	-3147.3776	6370.5073	0.0000	1.0000
JC69IG	37	-3147.0420	6372.0501	0.0000	1.0000
F81G	39	-3147.1720	6376.7569	0.0000	1.0000
F81IG	40	-3146.8327	6378.3112	0.0000	1.0000
JC69I	36	-3156.7335	6389.2191	0.0000	1.0000
F81I	39	-3156.5765	6395.5661	0.0000	1.0000
SYM	40	-3161.3564	6407.3586	0.0000	1.0000
GTR	43	-3160.8480	6413.0786	0.0000	1.0000
K2P	36	-3169.3926	6414.5373	0.0000	1.0000
HKY	39	-3169.1481	6420.7093	0.0000	1.0000
JC69	35	-3220.0282	6513.6006	0.0000	1.0000
F81	38	-3219.8679	6519.9223	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-3084.5876	6251.1752	0.6009	0.6009
SYMIG	42	-3084.1901	6252.3802	0.3289	0.9298
GTRG	44	-3084.2609	6256.5219	0.0415	0.9713
GTRIG	45	-3083.8586	6257.7172	0.0228	0.9941
K2PG	37	-3093.7214	6261.4427	0.0035	0.9976
K2PIG	38	-3093.3316	6262.6631	0.0019	0.9995
HKYG	40	-3093.2539	6266.5077	0.0003	0.9998
HKYIG	41	-3092.8519	6267.7038	0.0002	1.0000
SYMI	41	-3094.9214	6271.8428	0.0000	1.0000
GTRI	44	-3094.6499	6277.2998	0.0000	1.0000
K2PI	37	-3103.7560	6281.5120	0.0000	1.0000
HKYI	40	-3103.3705	6286.7411	0.0000	1.0000
JC69G	36	-3147.3776	6366.7552	0.0000	1.0000
JC69IG	37	-3147.0420	6368.0839	0.0000	1.0000
F81G	39	-3147.1720	6372.3439	0.0000	1.0000
F81IG	40	-3146.8327	6373.6653	0.0000	1.0000
JC69I	36	-3156.7335	6385.4669	0.0000	1.0000
F81I	39	-3156.5765	6391.1530	0.0000	1.0000
SYM	40	-3161.3564	6402.7127	0.0000	1.0000
GTR	43	-3160.8480	6407.6960	0.0000	1.0000
K2P	36	-3169.3926	6410.7852	0.0000	1.0000
HKY	39	-3169.1481	6416.2962	0.0000	1.0000
JC69	35	-3220.0282	6510.0563	0.0000	1.0000
F81	38	-3219.8679	6515.7359	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3093.7214	6432.2372	0.9331	0.9331
K2PIG	38	-3093.3316	6438.0736	0.0504	0.9835
SYMG	41	-3084.5876	6440.4339	0.0155	0.9990
SYMIG	42	-3084.1901	6446.2549	0.0008	0.9999
HKYG	40	-3093.2539	6451.1503	0.0001	1.0000
K2PI	37	-3103.7560	6452.3064	0.0000	1.0000
HKYIG	41	-3092.8519	6456.9624	0.0000	1.0000
GTRG	44	-3084.2609	6459.6287	0.0000	1.0000
SYMI	41	-3094.9214	6461.1015	0.0000	1.0000
GTRIG	45	-3083.8586	6465.4401	0.0000	1.0000
HKYI	40	-3103.3705	6471.3837	0.0000	1.0000
GTRI	44	-3094.6499	6480.4067	0.0000	1.0000
JC69G	36	-3147.3776	6532.9336	0.0000	1.0000
JC69IG	37	-3147.0420	6538.8783	0.0000	1.0000
JC69I	36	-3156.7335	6551.6453	0.0000	1.0000
F81G	39	-3147.1720	6552.3705	0.0000	1.0000
F81IG	40	-3146.8327	6558.3079	0.0000	1.0000
F81I	39	-3156.5765	6571.1796	0.0000	1.0000
K2P	36	-3169.3926	6576.9635	0.0000	1.0000
SYM	40	-3161.3564	6587.3553	0.0000	1.0000
HKY	39	-3169.1481	6596.3228	0.0000	1.0000
GTR	43	-3160.8480	6606.1868	0.0000	1.0000
JC69	35	-3220.0282	6671.6186	0.0000	1.0000
F81	38	-3219.8679	6691.1464	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_9442.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_9442.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_9442.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_9442.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=Fixed(Equal);
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/chr1_9442.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_9442.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

