
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:24 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/chrZ_5495.phylip" (19 taxa, 469 characters)

Minimum AIC  model: GTRI
Minimum AICc model: SYMI
Minimum BIC  model: SYMI


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
SYMI	41	-1364.3826	2818.8308	0.3558	0.3558
GTRI	44	-1361.1811	2819.7018	0.2302	0.5860
SYMG	41	-1364.9768	2820.0193	0.1964	0.7824
GTRG	44	-1361.8104	2820.9604	0.1227	0.9051
SYMIG	42	-1364.9770	2822.4329	0.0588	0.9638
GTRIG	45	-1361.8106	2823.4084	0.0361	0.9999
K2PI	37	-1378.2239	2836.9721	0.0000	1.0000
K2PG	37	-1378.6319	2837.7882	0.0000	1.0000
K2PIG	38	-1378.6320	2840.1570	0.0000	1.0000
HKYI	40	-1376.4746	2840.6127	0.0000	1.0000
HKYG	40	-1376.9462	2841.5559	0.0000	1.0000
HKYIG	41	-1376.9462	2843.9580	0.0000	1.0000
SYM	40	-1391.4238	2870.5111	0.0000	1.0000
GTR	43	-1388.5351	2871.9738	0.0000	1.0000
JC69I	36	-1401.9654	2882.0974	0.0000	1.0000
JC69G	36	-1402.3929	2882.9524	0.0000	1.0000
JC69IG	37	-1402.3929	2885.3101	0.0000	1.0000
F81I	39	-1400.6857	2886.6442	0.0000	1.0000
F81G	39	-1401.1358	2887.5443	0.0000	1.0000
K2P	36	-1404.9499	2888.0664	0.0000	1.0000
F81IG	40	-1401.1358	2889.9351	0.0000	1.0000
HKY	39	-1403.3732	2892.0191	0.0000	1.0000
JC69	35	-1428.2526	2932.3251	0.0000	1.0000
F81	38	-1426.9670	2936.8271	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1361.1811	2810.3622	0.3161	0.3161
SYMI	41	-1364.3826	2810.7652	0.2584	0.5745
GTRG	44	-1361.8104	2811.6208	0.1685	0.7429
SYMG	41	-1364.9768	2811.9537	0.1426	0.8855
GTRIG	45	-1361.8106	2813.6211	0.0620	0.9475
SYMIG	42	-1364.9770	2813.9540	0.0525	1.0000
K2PI	37	-1378.2239	2830.4478	0.0000	1.0000
K2PG	37	-1378.6319	2831.2638	0.0000	1.0000
HKYI	40	-1376.4746	2832.9491	0.0000	1.0000
K2PIG	38	-1378.6320	2833.2640	0.0000	1.0000
HKYG	40	-1376.9462	2833.8924	0.0000	1.0000
HKYIG	41	-1376.9462	2835.8925	0.0000	1.0000
SYM	40	-1391.4238	2862.8476	0.0000	1.0000
GTR	43	-1388.5351	2863.0703	0.0000	1.0000
JC69I	36	-1401.9654	2875.9307	0.0000	1.0000
JC69G	36	-1402.3929	2876.7858	0.0000	1.0000
JC69IG	37	-1402.3929	2878.7858	0.0000	1.0000
F81I	39	-1400.6857	2879.3714	0.0000	1.0000
F81G	39	-1401.1358	2880.2716	0.0000	1.0000
K2P	36	-1404.9499	2881.8998	0.0000	1.0000
F81IG	40	-1401.1358	2882.2715	0.0000	1.0000
HKY	39	-1403.3732	2884.7464	0.0000	1.0000
JC69	35	-1428.2526	2926.5052	0.0000	1.0000
F81	38	-1426.9670	2929.9341	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMI	41	-1364.3826	2980.9399	0.5142	0.5142
SYMG	41	-1364.9768	2982.1284	0.2838	0.7980
K2PI	37	-1378.2239	2984.0201	0.1102	0.9082
K2PG	37	-1378.6319	2984.8361	0.0733	0.9815
SYMIG	42	-1364.9770	2988.2794	0.0131	0.9946
K2PIG	38	-1378.6320	2990.9869	0.0034	0.9980
GTRI	44	-1361.1811	2992.9887	0.0012	0.9992
GTRG	44	-1361.8104	2994.2473	0.0007	0.9999
HKYI	40	-1376.4746	2998.9733	0.0001	0.9999
HKYG	40	-1376.9462	2999.9165	0.0000	1.0000
GTRIG	45	-1361.8106	3000.3982	0.0000	1.0000
HKYIG	41	-1376.9462	3006.0672	0.0000	1.0000
JC69I	36	-1401.9654	3025.3524	0.0000	1.0000
JC69G	36	-1402.3929	3026.2075	0.0000	1.0000
SYM	40	-1391.4238	3028.8717	0.0000	1.0000
K2P	36	-1404.9499	3031.3215	0.0000	1.0000
JC69IG	37	-1402.3929	3032.3581	0.0000	1.0000
F81I	39	-1400.6857	3041.2449	0.0000	1.0000
GTR	43	-1388.5351	3041.5462	0.0000	1.0000
F81G	39	-1401.1358	3042.1451	0.0000	1.0000
HKY	39	-1403.3732	3046.6199	0.0000	1.0000
F81IG	40	-1401.1358	3048.2957	0.0000	1.0000
JC69	35	-1428.2526	3071.7763	0.0000	1.0000
F81	38	-1426.9670	3087.6570	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5495.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

