
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:16 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_6778.phylip" (19 taxa, 311 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKY
Minimum BIC  model: HKY


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
HKY	39	-788.6571	1666.8271	0.2500	0.2500
HKYI	40	-787.3626	1666.8734	0.2443	0.4943
HKYG	40	-787.5555	1667.2591	0.2014	0.6957
GTRI	44	-783.1322	1669.1515	0.0782	0.7739
GTR	43	-784.5189	1669.2101	0.0759	0.8498
GTRG	44	-783.2708	1669.4288	0.0681	0.9179
HKYIG	41	-787.3684	1669.5397	0.0644	0.9823
GTRIG	45	-783.2535	1672.1297	0.0176	1.0000
K2P	36	-802.8000	1687.3226	0.0000	1.0000
K2PI	37	-801.5217	1687.3439	0.0000	1.0000
K2PG	37	-801.7644	1687.8292	0.0000	1.0000
SYMI	41	-797.0309	1688.8648	0.0000	1.0000
SYM	40	-798.3840	1688.9161	0.0000	1.0000
SYMG	41	-797.2509	1689.3047	0.0000	1.0000
K2PIG	38	-801.5291	1689.9553	0.0000	1.0000
SYMIG	42	-797.0382	1691.5541	0.0000	1.0000
F81	38	-803.7935	1694.4841	0.0000	1.0000
F81I	39	-802.6123	1694.7376	0.0000	1.0000
F81G	39	-802.8020	1695.1169	0.0000	1.0000
F81IG	40	-802.6183	1697.3848	0.0000	1.0000
JC69	35	-816.7867	1712.7370	0.0000	1.0000
JC69I	36	-815.5952	1712.9131	0.0000	1.0000
JC69G	36	-815.8150	1713.3526	0.0000	1.0000
JC69IG	37	-815.6022	1715.5048	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-783.1322	1654.2643	0.1921	0.1921
GTRG	44	-783.2708	1654.5416	0.1672	0.3592
HKYI	40	-787.3626	1654.7252	0.1525	0.5118
GTR	43	-784.5189	1655.0379	0.1305	0.6422
HKYG	40	-787.5555	1655.1109	0.1258	0.7680
HKY	39	-788.6571	1655.3142	0.1136	0.8816
GTRIG	45	-783.2535	1656.5070	0.0626	0.9442
HKYIG	41	-787.3684	1656.7367	0.0558	1.0000
SYMI	41	-797.0309	1676.0618	0.0000	1.0000
SYMG	41	-797.2509	1676.5018	0.0000	1.0000
SYM	40	-798.3840	1676.7680	0.0000	1.0000
K2PI	37	-801.5217	1677.0435	0.0000	1.0000
K2PG	37	-801.7644	1677.5288	0.0000	1.0000
K2P	36	-802.8000	1677.5999	0.0000	1.0000
SYMIG	42	-797.0382	1678.0764	0.0000	1.0000
K2PIG	38	-801.5291	1679.0583	0.0000	1.0000
F81I	39	-802.6123	1683.2247	0.0000	1.0000
F81	38	-803.7935	1683.5871	0.0000	1.0000
F81G	39	-802.8020	1683.6040	0.0000	1.0000
F81IG	40	-802.6183	1685.2366	0.0000	1.0000
JC69I	36	-815.5952	1703.1905	0.0000	1.0000
JC69	35	-816.7867	1703.5734	0.0000	1.0000
JC69G	36	-815.8150	1703.6299	0.0000	1.0000
JC69IG	37	-815.6022	1705.2044	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-788.6571	1801.1661	0.7165	0.7165
HKYI	40	-787.3626	1804.3170	0.1483	0.8648
HKYG	40	-787.5555	1804.7027	0.1223	0.9871
HKYIG	41	-787.3684	1810.0682	0.0084	0.9954
K2P	36	-802.8000	1812.2325	0.0028	0.9983
K2PI	37	-801.5217	1815.4158	0.0006	0.9988
GTR	43	-784.5189	1815.8490	0.0005	0.9993
K2PG	37	-801.7644	1815.9012	0.0005	0.9998
GTRI	44	-783.1322	1818.8152	0.0001	0.9999
GTRG	44	-783.2708	1819.0925	0.0001	1.0000
K2PIG	38	-801.5291	1821.1704	0.0000	1.0000
GTRIG	45	-783.2535	1824.7977	0.0000	1.0000
F81	38	-803.7935	1825.6992	0.0000	1.0000
SYM	40	-798.3840	1826.3597	0.0000	1.0000
F81I	39	-802.6123	1829.0766	0.0000	1.0000
SYMI	41	-797.0309	1829.3933	0.0000	1.0000
F81G	39	-802.8020	1829.4559	0.0000	1.0000
SYMG	41	-797.2509	1829.8333	0.0000	1.0000
JC69	35	-816.7867	1834.4661	0.0000	1.0000
F81IG	40	-802.6183	1834.8284	0.0000	1.0000
SYMIG	42	-797.0382	1835.1477	0.0000	1.0000
JC69I	36	-815.5952	1837.8230	0.0000	1.0000
JC69G	36	-815.8150	1838.2625	0.0000	1.0000
JC69IG	37	-815.6022	1843.5768	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_6778.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6778.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 (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6778.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6778.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6778.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6778.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

