
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:51 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/chr7_10378.phylip" (19 taxa, 189 characters)

Minimum AIC  model: K2PI
Minimum AICc model: K2PI
Minimum BIC  model: K2PI


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
K2PI	37	-407.0307	906.6839	0.3292	0.3292
K2PG	37	-407.0430	906.7086	0.3251	0.6543
K2PIG	38	-407.0312	909.8223	0.0685	0.7229
JC69I	36	-410.2299	909.9861	0.0632	0.7860
JC69G	36	-410.2379	910.0021	0.0626	0.8487
HKYI	40	-404.4049	910.9720	0.0386	0.8872
HKYG	40	-404.4278	911.0179	0.0377	0.9249
K2P	36	-411.0605	911.6474	0.0275	0.9525
JC69IG	37	-410.2299	913.0823	0.0134	0.9659
HKYIG	41	-404.4051	914.2387	0.0075	0.9734
F81I	39	-407.7816	914.5028	0.0066	0.9800
F81G	39	-407.7931	914.5258	0.0065	0.9865
JC69	35	-414.2074	914.8853	0.0055	0.9920
HKY	39	-408.5719	916.0834	0.0030	0.9950
F81IG	40	-407.7817	917.7255	0.0013	0.9963
SYMI	41	-406.1848	917.7981	0.0013	0.9976
SYMG	41	-406.1883	917.8051	0.0013	0.9988
F81	38	-411.8161	919.3922	0.0006	0.9994
SYMIG	42	-406.1849	921.1096	0.0002	0.9997
SYM	40	-410.0874	922.3369	0.0001	0.9998
GTRI	44	-403.7484	922.9967	0.0001	0.9999
GTRG	44	-403.7567	923.0134	0.0001	1.0000
GTRIG	45	-403.7484	926.4479	0.0000	1.0000
GTR	43	-407.7435	927.5835	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
K2PI	37	-407.0307	888.0614	0.2161	0.2161
K2PG	37	-407.0430	888.0860	0.2134	0.4295
HKYI	40	-404.4049	888.8098	0.1486	0.5781
HKYG	40	-404.4278	888.8557	0.1452	0.7233
K2PIG	38	-407.0312	890.0623	0.0794	0.8027
HKYIG	41	-404.4051	890.8101	0.0547	0.8574
JC69I	36	-410.2299	892.4597	0.0240	0.8814
JC69G	36	-410.2379	892.4758	0.0238	0.9051
F81I	39	-407.7816	893.5632	0.0138	0.9189
F81G	39	-407.7931	893.5862	0.0136	0.9326
K2P	36	-411.0605	894.1211	0.0104	0.9430
SYMI	41	-406.1848	894.3695	0.0092	0.9522
SYMG	41	-406.1883	894.3765	0.0092	0.9614
JC69IG	37	-410.2299	894.4598	0.0088	0.9702
HKY	39	-408.5719	895.1438	0.0063	0.9765
GTRI	44	-403.7484	895.4967	0.0052	0.9817
GTRG	44	-403.7567	895.5134	0.0052	0.9869
F81IG	40	-407.7817	895.5634	0.0051	0.9920
SYMIG	42	-406.1849	896.3698	0.0034	0.9954
GTRIG	45	-403.7484	897.4968	0.0019	0.9973
JC69	35	-414.2074	898.4147	0.0012	0.9986
F81	38	-411.8161	899.6322	0.0007	0.9992
SYM	40	-410.0874	900.1747	0.0005	0.9997
GTR	43	-407.7435	901.4869	0.0003	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-407.0307	1008.0060	0.2758	0.2758
K2PG	37	-407.0430	1008.0307	0.2725	0.5483
JC69I	36	-410.2299	1009.1626	0.1547	0.7030
JC69G	36	-410.2379	1009.1787	0.1535	0.8565
K2P	36	-411.0605	1010.8240	0.0674	0.9239
JC69	35	-414.2074	1011.8759	0.0398	0.9637
K2PIG	38	-407.0312	1013.2487	0.0201	0.9838
JC69IG	37	-410.2299	1014.4044	0.0113	0.9951
HKYI	40	-404.4049	1018.4797	0.0015	0.9965
HKYG	40	-404.4278	1018.5256	0.0014	0.9980
F81I	39	-407.7816	1019.9913	0.0007	0.9986
F81G	39	-407.7931	1020.0144	0.0007	0.9993
HKY	39	-408.5719	1021.5719	0.0003	0.9996
F81	38	-411.8161	1022.8186	0.0002	0.9998
HKYIG	41	-404.4051	1023.7217	0.0001	0.9999
F81IG	40	-407.7817	1025.2332	0.0001	1.0000
SYMI	41	-406.1848	1027.2812	0.0000	1.0000
SYMG	41	-406.1883	1027.2881	0.0000	1.0000
SYM	40	-410.0874	1029.8446	0.0000	1.0000
SYMIG	42	-406.1849	1032.5232	0.0000	1.0000
GTRI	44	-403.7484	1038.1336	0.0000	1.0000
GTRG	44	-403.7567	1038.1503	0.0000	1.0000
GTR	43	-407.7435	1040.8821	0.0000	1.0000
GTRIG	45	-403.7484	1043.3754	0.0000	1.0000



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

[Mrbayes block for the best AIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip = 1 - 189;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip = 1 - 189;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip = 1 - 189;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10378.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

