MCMC Post-hoc Analysis: 25 sequences

Data & Model

Partition	Sequences	Lengths	Alphabet	Substitution Model	Indel Model	Scale Model
1	25.fasta	111 - 131	RNA	S1 = gtr+Rates.gamma[4]+inv	I1 = rs07	scale1 ~ gamma[0.5,2,0.0]

Scalar variables

Statistic	Median	95% BCI	ACT	ESS	burnin	PSRF-CI80%	PSRF-RCF
prior	-330.5	(-383.1, -283.6)	40.2	35818	523	1	1.001
prior_A1	-427.4	(-476.8, -384.3)	39.98	36016	371	1	1
likelihood	-2695	(-2723, -2668)	59.99	24003	218	1	1.001
posterior	-3026	(-3071, -2986)	16.58	86871	439	1	1.003
Heat.beta	1
Scale[1]	9.422	(6.138, 13.54)	2.122	678581	266	0.9999	0.9979
gtr:pi[A]	0.2135	(0.1743, 0.2566)	15.89	90629	631	1	0.9998
gtr:pi[C]	0.2852	(0.2448, 0.3276)	16.53	87128	248	1	0.9998
gtr:pi[G]	0.3049	(0.2593, 0.353)	12.54	114860	402	1	0.9992
gtr:pi[U]	0.1939	(0.1635, 0.226)	30.38	47400	650	1	0.9992
gtr:sym[AC]	0.03505	(0.003978, 0.06984)	10.94	131671	297	0.9998	1.004
gtr:sym[AG]	0.1627	(0.1123, 0.2193)	16.57	86881	402	1	1.005
gtr:sym[AU]	0.2859	(0.2087, 0.3665)	13.39	107537	519	1	0.999
gtr:sym[CG]	0.08263	(0.04476, 0.1242)	29.81	48306	715	1	0.9972
gtr:sym[CU]	0.3505	(0.2727, 0.4333)	14.85	96950	430	1	1.002
gtr:sym[GU]	0.07562	(0.03661, 0.1196)	21.76	66190	479	1	0.999
Rates.gamma:alpha	1.538	(0.9609, 2.256)	5.22	275871	253	0.9999	1.002
inv:p_inv	0.1338	(0.06288, 0.2113)	2.553	563974	156	1	0.999
rs07:mean_length	2.179	(1.676, 2.838)	100.3	14360	259	1	1.001
rs07:log_rate	-3.857	(-4.196, -3.503)	7.061	203939	194	1	0.9998
|A1|	173	(158, 197)	495.3	2907	7215	0.9774	0.9964
#indels1	57	(50, 65)	18.16	79274	371	0.8633	1.002
|indels1|	120	(99, 144)	215.6	6679	1077	0.9917	0.9981
#substs1	714	(694, 730)	149	9667	489	0.9684	0.9977
Scale1*|T|	10.97	(8.809, 13.52)	7.433	193729	233	1	0.9988
|A|	173	(158, 197)	495.3	2907	7215	0.9774	0.9964
#indels	57	(50, 65)	18.16	79274	371	0.8633	1.002
|indels|	120	(99, 144)	215.6	6679	1077	0.9917	0.9981
#substs	714	(694, 730)	149	9667	489	0.9684	0.9977
|T|	1.169	(0.7907, 1.596)	1.008	1429089	168	1	0.9984

Phylogeny Distribution

Partition support: Summary

Partition support graph: SVG

50% consensus	Newick (+PP)	PDF	SVG
66% consensus	Newick (+PP)	PDF	SVG
80% consensus	Newick (+PP)	PDF	SVG
90% consensus	Newick (+PP)	PDF	SVG
95% consensus	Newick (+PP)	PDF	SVG
99% consensus	Newick (+PP)	PDF	SVG
100% consensus	Newick (+PP)	PDF	SVG
MAP	Newick (+PP)	PDF	SVG
greedy	Newick (+PP)	PDF	SVG

Alignment Distribution

Partition 1

			Diff		Min. %identity	# Sites	Constant	Informative
Initial	FASTA	HTML	Diff		12.7%	131	0 (0%)	126 (96.2%)
Best (WPD)	FASTA	HTML		AU	31.5%	198	11 (5.56%)	123 (62.1%)

Mixing

1. Partition uncertainty
2. SRQ plot: partitions
3. SRQ plot: c50
4. Variation in split frequency estimates

burnin (scalar)	ESS (scalar)	ESS (partition)	ASDSF	MSDSF	PSRF-CI80%	PSRF-RCF
7215	2908	6698.038	0.004	0.017	1	1.005

Projection of RF distances for the first 3 chains (Hillis et al 2005) 3D

Variation of split PPs across chains (Beiko et al 2006)

---

Analysis

command line: bali-phy 25.fasta -S gtr+Rates.gamma+inv

directory: /gpfs/fs0/data/wraycompute/br51/Work/3.1

chain #	burnin	subsample	Iterations (after burnin)	subdirectory
1	20000	1	180000	25-1
2	20000	1	180000	25-2
3	20000	1	180000	25-3
4	20000	1	180000	25-4
5	20000	1	180000	25-5
6	20000	1	180000	25-6
7	20000	1	180000	25-7
8	20000	1	180000	25-8

P(data|M) = -2723.519 +- 0.211

Complete sample: 1529699 topologies

95% Bayesian credible interval: 1449809 topologies

Model and priors

Tree (+priors)

topology	~ uniform on tree topologies
branch lengths	~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]],0.0]]

Substitution model (+priors)

S1

=

gtr+Rates.gamma[4]+inv gtr:sym ~ dirichlet_on[letter_pairs[a],1] gtr:pi ~ dirichlet_on[letters[a],1] Rates.gamma:alpha ~ log_laplace[6,2] inv:p_inv ~ uniform[0,1]

Indel model (+priors)

I1

=

rs07 rs07:log_rate ~ laplace[-4,0.707] rs07:mean_length ~ exponential[10,1]

Scales (+priors)

scale1

~

gamma[0.5,2,0.0]