
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:31 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_6396.phylip" (19 taxa, 821 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3302.3487	6697.8006	0.9327	0.9327
HKYI	40	-3310.1403	6704.4858	0.0330	0.9657
HKYG	40	-3310.4745	6705.1542	0.0236	0.9893
HKYIG	41	-3310.3643	6707.1496	0.0087	0.9980
GTRI	44	-3308.7059	6710.5148	0.0016	0.9996
GTRIG	45	-3308.9512	6713.2444	0.0004	1.0000
K2PI	37	-3325.3715	6728.3342	0.0000	1.0000
K2PG	37	-3326.1633	6729.9180	0.0000	1.0000
SYMI	41	-3321.9587	6730.3386	0.0000	1.0000
K2PIG	38	-3326.0656	6731.9215	0.0000	1.0000
SYMG	41	-3322.7666	6731.9543	0.0000	1.0000
SYMIG	42	-3322.6583	6733.9593	0.0000	1.0000
HKY	39	-3366.0307	6814.0562	0.0000	1.0000
GTR	43	-3364.5775	6820.0250	0.0000	1.0000
F81G	39	-3375.5200	6833.0349	0.0000	1.0000
F81IG	40	-3375.4996	6835.2043	0.0000	1.0000
K2P	36	-3380.5012	6836.4003	0.0000	1.0000
SYM	40	-3377.1661	6838.5373	0.0000	1.0000
F81I	39	-3380.8386	6843.6722	0.0000	1.0000
JC69G	36	-3389.1250	6853.6479	0.0000	1.0000
JC69IG	37	-3389.1142	6855.8198	0.0000	1.0000
JC69I	36	-3394.2698	6863.9376	0.0000	1.0000
F81	38	-3435.1645	6950.1193	0.0000	1.0000
JC69	35	-3448.0822	6969.3747	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3302.3487	6692.6975	0.9546	0.9546
HKYI	40	-3310.1403	6700.2807	0.0215	0.9761
HKYG	40	-3310.4745	6700.9491	0.0154	0.9915
HKYIG	41	-3310.3643	6702.7285	0.0063	0.9979
GTRI	44	-3308.7059	6705.4117	0.0017	0.9995
GTRIG	45	-3308.9512	6707.9025	0.0005	1.0000
K2PI	37	-3325.3715	6724.7429	0.0000	1.0000
SYMI	41	-3321.9587	6725.9175	0.0000	1.0000
K2PG	37	-3326.1633	6726.3267	0.0000	1.0000
SYMG	41	-3322.7666	6727.5332	0.0000	1.0000
K2PIG	38	-3326.0656	6728.1313	0.0000	1.0000
SYMIG	42	-3322.6583	6729.3166	0.0000	1.0000
HKY	39	-3366.0307	6810.0614	0.0000	1.0000
GTR	43	-3364.5775	6815.1550	0.0000	1.0000
F81G	39	-3375.5200	6829.0400	0.0000	1.0000
F81IG	40	-3375.4996	6830.9991	0.0000	1.0000
K2P	36	-3380.5012	6833.0023	0.0000	1.0000
SYM	40	-3377.1661	6834.3321	0.0000	1.0000
F81I	39	-3380.8386	6839.6773	0.0000	1.0000
JC69G	36	-3389.1250	6850.2500	0.0000	1.0000
JC69IG	37	-3389.1142	6852.2284	0.0000	1.0000
JC69I	36	-3394.2698	6860.5396	0.0000	1.0000
F81	38	-3435.1645	6946.3291	0.0000	1.0000
JC69	35	-3448.0822	6966.1645	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-3310.1403	6888.7016	0.5695	0.5695
HKYG	40	-3310.4745	6889.3700	0.4077	0.9773
HKYIG	41	-3310.3643	6895.8599	0.0159	0.9932
K2PI	37	-3325.3715	6899.0323	0.0033	0.9964
GTRG	44	-3302.3487	6899.9605	0.0020	0.9985
K2PG	37	-3326.1633	6900.6160	0.0015	0.9999
K2PIG	38	-3326.0656	6907.1311	0.0001	1.0000
GTRI	44	-3308.7059	6912.6747	0.0000	1.0000
SYMI	41	-3321.9587	6919.0489	0.0000	1.0000
GTRIG	45	-3308.9512	6919.8760	0.0000	1.0000
SYMG	41	-3322.7666	6920.6647	0.0000	1.0000
SYMIG	42	-3322.6583	6927.1586	0.0000	1.0000
HKY	39	-3366.0307	6993.7718	0.0000	1.0000
K2P	36	-3380.5012	7002.5812	0.0000	1.0000
F81G	39	-3375.5200	7012.7504	0.0000	1.0000
GTR	43	-3364.5775	7017.7075	0.0000	1.0000
F81IG	40	-3375.4996	7019.4201	0.0000	1.0000
JC69G	36	-3389.1250	7019.8288	0.0000	1.0000
SYM	40	-3377.1661	7022.7531	0.0000	1.0000
F81I	39	-3380.8386	7023.3877	0.0000	1.0000
JC69IG	37	-3389.1142	7026.5178	0.0000	1.0000
JC69I	36	-3394.2698	7030.1185	0.0000	1.0000
F81	38	-3435.1645	7125.3289	0.0000	1.0000
JC69	35	-3448.0822	7131.0328	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/chrZ_6396.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6396.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/chrZ_6396.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6396.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6396.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6396.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

