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|
Running GARLI-PART Version 2.0.1008 (17 Mar 2011)
->Single processor version<-
##############################################################
This is GARLI 2.0, the first "official" release including
partitioned models. It is a merging of
official release 1.0 and beta version GARLI-PART 0.97
Briefly, it includes models for nucleotides, amino acids,
codons, and morphology-like characters, any of which can be
mixed together and applied to different subsets of data.
General program usage is extensively documented here:
http://www.nescent.org/wg_garli/
see this page for details on partitioned usage:
http://www.nescent.org/wg_garli/Partition_testing_version
and this page for details on Mkv mophology model usage:
http://www.nescent.org/wg_garli/Mkv_morphology_model
PLEASE LET ME KNOW OF ANY PROBLEMS AT:
garli.support@gmail.com
##############################################################
This version has undergone much testing, but is still a BETA VERSION.
- Please check results carefully! -
Compiled Mar 21 2011 13:13:18 using Intel icc compiler version 9.10
Using NCL version 2.1.10
#######################################################
Reading config file garli.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
lewis2001.nex ...
Reading CHARACTERS block... found standard data... successful
Reading ASSUMPTIONS block... successful
###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
Data read as Standard k-state data, variable only,
modeled as Standard k-state data, variable only
Subset of data with 2 states:
chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
Summary of data:
30 sequences.
0 constant characters.
39 parsimony-informative characters.
0 uninformative variable characters.
39 total characters.
39 unique patterns in compressed data matrix.
Pattern processing required < 1 second
Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
char 90
Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
char 90
Subset of data with 3 states:
chars 54 61 62 64 71 72 83 90-102 \ 6
Summary of data:
30 sequences.
0 constant characters.
10 parsimony-informative characters.
0 uninformative variable characters.
10 total characters.
10 unique patterns in compressed data matrix.
Pattern processing required < 1 second
Subset of data with 4 states:
chars 52 59 73
Summary of data:
30 sequences.
0 constant characters.
0 parsimony-informative characters.
3 uninformative variable characters.
3 total characters.
3 unique patterns in compressed data matrix.
Pattern processing required < 1 second
NOTE: No characters found with 5 observed states.
NOTE: No characters found with 6 observed states.
###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of
physical memory that your computer has installed)
For this dataset:
Mem level availablememory setting
great >= 1 MB
good approx 0 MB to 1 MB
low approx 0 MB to 1 MB
very low approx 0 MB to 1 MB
the minimum required availablememory is 1 MB
You specified that Garli should use at most 512.0 MB of memory.
Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**
#######################################################
STARTING RUN
>>>Search rep 1 (of 5)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Starting with seed=113156
creating random starting tree...
NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.
Initial ln Likelihood: -1296.0557
optimizing: starting branch lengths...
pass 1:+ 364.588 (branch= 364.59 scale= 0.00)
pass 2:+ 66.578 (branch= 63.37 scale= 3.21)
pass 3:+ 24.948 (branch= 23.25 scale= 1.69)
pass 4:+ 1.187 (branch= 0.53 scale= 0.66)
pass 5:+ 1.040 (branch= 1.04 scale= 0.00)
pass 6:+ 0.000 (branch= 0.00 scale= 0.00)
lnL after optimization: -837.7145
gen current_lnL precision last_tree_imp
0 -837.7145 0.500 0
100 -592.1303 0.500 95
200 -550.9261 0.500 198
300 -502.7223 0.500 293
400 -496.2153 0.500 379
500 -482.5724 0.500 480
600 -480.2205 0.500 599
700 -479.5176 0.500 599
800 -479.0438 0.500 706
900 -478.6735 0.500 706
1000 -478.3272 0.500 706
1100 -477.8447 0.500 1006
1200 -476.5510 0.500 1153
1300 -476.0617 0.500 1153
1400 -475.8286 0.500 1153
1500 -475.5767 0.500 1153
1600 -475.4253 0.500 1153
1700 -475.2730 0.500 1153
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.002 lnL
1800 -475.1729 0.451 1153
1900 -475.1232 0.451 1153
2000 -474.7475 0.451 1914
2100 -474.6530 0.451 1914
2200 -474.3547 0.451 2182
2300 -474.2897 0.451 2182
2400 -474.1635 0.451 2182
2500 -474.1124 0.451 2182
2600 -474.0612 0.451 2182
2700 -473.9885 0.451 2182
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
2800 -473.9058 0.402 2744
2900 -473.7521 0.402 2846
3000 -473.7250 0.402 2846
3100 -473.6863 0.402 2846
3200 -473.6766 0.402 2846
3300 -473.6522 0.402 2846
3400 -473.6455 0.402 2846
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3500 -473.6274 0.353 2846
3600 -473.5061 0.353 3576
3700 -473.4862 0.353 3576
3800 -473.4791 0.353 3576
3900 -473.4632 0.353 3576
4000 -473.4431 0.353 3576
4100 -473.4328 0.353 3576
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4200 -473.4217 0.304 3576
4300 -473.4091 0.304 3576
4400 -473.3964 0.304 3576
4500 -473.3896 0.304 3576
4600 -473.3704 0.304 4588
4700 -473.3686 0.304 4588
4800 -473.3595 0.304 4588
4900 -473.3544 0.304 4588
5000 -473.3466 0.304 4588
5100 -473.3397 0.304 4588
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5200 -473.3341 0.255 4588
5300 -473.3251 0.255 4588
5400 -473.3183 0.255 4588
5500 -473.2540 0.255 5457
5600 -473.1386 0.255 5457
5700 -473.0787 0.255 5457
5800 -473.0601 0.255 5457
5900 -473.0481 0.255 5457
6000 -472.9455 0.255 5996
6100 -472.9401 0.255 5996
6200 -472.9357 0.255 5996
6300 -472.9343 0.255 5996
6400 -472.9339 0.255 5996
6500 -472.9274 0.255 5996
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
6600 -472.9270 0.206 5996
6700 -472.9227 0.206 5996
6800 -472.9208 0.206 5996
6900 -472.9158 0.206 5996
7000 -472.9152 0.206 5996
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
7100 -472.9117 0.157 5996
7200 -472.8881 0.157 7137
7300 -472.8873 0.157 7137
7400 -472.8860 0.157 7137
7500 -472.8830 0.157 7137
7600 -472.8824 0.157 7137
7700 -472.8805 0.157 7137
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.168 lnL
7800 -472.6943 0.108 7137
7900 -472.6573 0.108 7137
8000 -472.6449 0.108 7137
8100 -472.6326 0.108 7137
8200 -472.6290 0.108 7137
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
8300 -472.6197 0.059 7137
8400 -472.5536 0.059 8357
8500 -472.5409 0.059 8357
8600 -472.5364 0.059 8357
8700 -472.5310 0.059 8357
8800 -472.5256 0.059 8357
8900 -472.5249 0.059 8357
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.066 lnL
9000 -472.4570 0.010 8357
9100 -472.4491 0.010 8357
9200 -472.4424 0.010 8357
9300 -472.4399 0.010 8357
9400 -472.4338 0.010 8357
9500 -472.4322 0.010 8357
9600 -472.4291 0.010 8357
9700 -472.4275 0.010 8357
9800 -472.4256 0.010 8357
9900 -472.4229 0.010 8357
10000 -472.4203 0.010 8357
10100 -472.4203 0.010 8357
10200 -472.4200 0.010 8357
10300 -472.4200 0.010 8357
10400 -472.4197 0.010 8357
10500 -472.4191 0.010 8357
10600 -472.4179 0.010 8357
10700 -472.4176 0.010 8357
10800 -472.4172 0.010 8357
10900 -472.4136 0.010 8357
11000 -472.4115 0.010 8357
11100 -472.4102 0.010 8357
11200 -472.4099 0.010 8357
11300 -472.4096 0.010 8357
11400 -472.4092 0.010 8357
11500 -472.4087 0.010 8357
11600 -472.4086 0.010 8357
11700 -472.4082 0.010 8357
11800 -472.4080 0.010 8357
11900 -472.4078 0.010 8357
12000 -472.4075 0.010 8357
12100 -472.4074 0.010 8357
12200 -472.4073 0.010 8357
12300 -472.4068 0.010 8357
12400 -472.4066 0.010 8357
12500 -472.4065 0.010 8357
12600 -472.4064 0.010 8357
12700 -472.4060 0.010 8357
12800 -472.4059 0.010 8357
12900 -472.4058 0.010 8357
13000 -472.4057 0.010 8357
13100 -472.4056 0.010 8357
13200 -472.4056 0.010 8357
13300 -472.4056 0.010 8357
13400 -472.4055 0.010 8357
13500 -472.4054 0.010 8357
13600 -472.4054 0.010 8357
13700 -472.4054 0.010 8357
13800 -472.4053 0.010 8357
13900 -472.4052 0.010 8357
14000 -472.4052 0.010 8357
14100 -472.4048 0.010 8357
14200 -472.4048 0.010 8357
14300 -472.4047 0.010 8357
14400 -472.4045 0.010 8357
14500 -472.4045 0.010 8357
14600 -472.4045 0.010 8357
14700 -472.4045 0.010 8357
14800 -472.4045 0.010 8357
14900 -472.4045 0.010 8357
15000 -472.4044 0.010 8357
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
15100 -472.4042 0.010 8357
15200 -472.4042 0.010 8357
15300 -472.4041 0.010 8357
15400 -472.4041 0.010 8357
15500 -472.4039 0.010 8357
15600 -472.4039 0.010 8357
15700 -472.4036 0.010 8357
15800 -472.4036 0.010 8357
15900 -472.4034 0.010 8357
16000 -472.4034 0.010 8357
16100 -472.4032 0.010 8357
16200 -472.4031 0.010 8357
16300 -472.4031 0.010 8357
16400 -472.4031 0.010 8357
16500 -472.4030 0.010 8357
16600 -472.4028 0.010 8357
16700 -472.4028 0.010 8357
16800 -472.4027 0.010 8357
16900 -472.4027 0.010 8357
17000 -472.4026 0.010 8357
17100 -472.4026 0.010 8357
17200 -472.4025 0.010 8357
17300 -472.4025 0.010 8357
17400 -472.4024 0.010 8357
17500 -472.4022 0.010 8357
17600 -472.4022 0.010 8357
17700 -472.4022 0.010 8357
17800 -472.4021 0.010 8357
17900 -472.4020 0.010 8357
18000 -472.4020 0.010 8357
18100 -472.4020 0.010 8357
18200 -472.4020 0.010 8357
18300 -472.4019 0.010 8357
18400 -472.4018 0.010 8357
18500 -472.4018 0.010 8357
18600 -472.4017 0.010 8357
18700 -472.4015 0.010 8357
18800 -472.4014 0.010 8357
18900 -472.4014 0.010 8357
19000 -472.4014 0.010 8357
Reached termination condition!
last topological improvement at gen 8357
Improvement over last 500 gen = 0.00042
Current score = -472.4014
Performing final optimizations...
pass 1 : -472.4014 (branch= 0.0000)
pass 2 : -472.4014 (branch= 0.0000)
pass 3 : -472.3948 (branch= 0.0066)
pass 4 : -472.3919 (branch= 0.0029)
pass 5 : -472.3915 (branch= 0.0004)
pass 6 : -472.3915 (branch= 0.0000)
pass 7 : -472.3915 (branch= 0.0000)
pass 8 : -472.3912 (branch= 0.0003)
pass 9 : -472.3910 (branch= 0.0002)
pass 10: -472.3909 (branch= 0.0001)
pass 11: -472.3908 (branch= 0.0000)
pass 12: -472.3908 (branch= 0.0000)
pass 13: -472.3908 (branch= 0.0000)
Looking for minimum length branches...
Final score = -472.3908
Time used so far = 0 hours, 0 minutes and 50 seconds
MODEL REPORT - Parameter values are FINAL
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
8 branches were collapsed.
>>>Completed Search rep 1 (of 5)<<<
>>>Search rep 2 (of 5)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Starting with seed=44926809
creating random starting tree...
Initial ln Likelihood: -1318.0450
optimizing: starting branch lengths...
pass 1:+ 430.059 (branch= 430.06 scale= 0.00)
pass 2:+ 43.968 (branch= 37.57 scale= 6.40)
pass 3:+ 15.540 (branch= 12.62 scale= 2.92)
pass 4:+ 13.620 (branch= 10.43 scale= 3.19)
pass 5:+ 2.101 (branch= 1.37 scale= 0.73)
pass 6:+ 0.440 (branch= 0.44 scale= 0.00)
lnL after optimization: -812.3165
gen current_lnL precision last_tree_imp
0 -812.3165 0.500 0
100 -631.8927 0.500 95
200 -515.5765 0.500 183
300 -513.6662 0.500 281
400 -495.7026 0.500 389
500 -489.8560 0.500 486
600 -487.9821 0.500 540
700 -487.2379 0.500 695
800 -477.6723 0.500 794
900 -477.1914 0.500 832
1000 -476.5205 0.500 982
1100 -475.5301 0.500 1044
1200 -475.2139 0.500 1044
1300 -474.8837 0.500 1044
1400 -474.6604 0.500 1044
1500 -474.3814 0.500 1044
1600 -474.1658 0.500 1044
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.079 lnL
1700 -473.9456 0.451 1044
1800 -473.8144 0.451 1044
1900 -473.6242 0.451 1883
2000 -473.2478 0.451 1883
2100 -473.1190 0.451 1883
2200 -473.0786 0.451 1883
2300 -473.0143 0.451 1883
2400 -472.9732 0.451 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
2500 -472.9234 0.402 1883
2600 -472.8918 0.402 1883
2700 -472.8750 0.402 1883
2800 -472.8232 0.402 1883
2900 -472.8046 0.402 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3000 -472.7937 0.353 1883
3100 -472.7611 0.353 1883
3200 -472.7356 0.353 1883
3300 -472.7169 0.353 1883
3400 -472.7028 0.353 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3500 -472.6782 0.304 1883
3600 -472.6583 0.304 1883
3700 -472.6535 0.304 1883
3800 -472.6366 0.304 1883
3900 -472.6268 0.304 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4000 -472.6163 0.255 1883
4100 -472.5964 0.255 1883
4200 -472.5787 0.255 1883
4300 -472.5698 0.255 1883
4400 -472.5472 0.255 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4500 -472.5449 0.206 1883
4600 -472.5388 0.206 1883
4700 -472.5311 0.206 1883
4800 -472.5289 0.206 1883
4900 -472.5262 0.206 1883
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5000 -472.5023 0.157 4939
5100 -472.4963 0.157 4939
5200 -472.4951 0.157 4939
5300 -472.4922 0.157 4939
5400 -472.4812 0.157 4939
5500 -472.4718 0.157 4939
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5600 -472.4685 0.108 4939
5700 -472.4673 0.108 4939
5800 -472.4662 0.108 4939
5900 -472.4640 0.108 4939
6000 -472.4630 0.108 4939
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
6100 -472.4625 0.059 4939
6200 -472.4612 0.059 4939
6300 -472.4563 0.059 4939
6400 -472.4541 0.059 4939
6500 -472.4538 0.059 4939
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.038 lnL
6600 -472.4158 0.010 4939
6700 -472.4158 0.010 4939
6800 -472.4154 0.010 4939
6900 -472.4151 0.010 4939
7000 -472.4147 0.010 4939
7100 -472.4139 0.010 4939
7200 -472.4137 0.010 4939
7300 -472.4130 0.010 4939
7400 -472.4130 0.010 4939
7500 -472.4106 0.010 4939
7600 -472.4105 0.010 4939
7700 -472.4103 0.010 4939
7800 -472.4101 0.010 4939
7900 -472.4098 0.010 4939
8000 -472.4094 0.010 4939
8100 -472.4093 0.010 4939
8200 -472.4093 0.010 4939
8300 -472.4090 0.010 4939
8400 -472.4089 0.010 4939
8500 -472.4087 0.010 4939
8600 -472.4086 0.010 4939
8700 -472.4085 0.010 4939
8800 -472.4084 0.010 4939
8900 -472.4083 0.010 4939
9000 -472.4081 0.010 4939
9100 -472.4080 0.010 4939
9200 -472.4080 0.010 4939
9300 -472.4078 0.010 4939
9400 -472.4076 0.010 4939
9500 -472.4072 0.010 4939
9600 -472.4071 0.010 4939
9700 -472.4067 0.010 4939
9800 -472.4067 0.010 4939
9900 -472.4067 0.010 4939
10000 -472.4066 0.010 4939
10100 -472.4063 0.010 4939
10200 -472.4061 0.010 4939
10300 -472.4060 0.010 4939
10400 -472.4060 0.010 4939
10500 -472.4060 0.010 4939
10600 -472.4058 0.010 4939
10700 -472.4058 0.010 4939
10800 -472.4056 0.010 4939
10900 -472.4055 0.010 4939
11000 -472.4054 0.010 4939
11100 -472.4052 0.010 4939
11200 -472.4052 0.010 4939
11300 -472.4052 0.010 4939
11400 -472.4051 0.010 4939
11500 -472.4050 0.010 4939
11600 -472.4050 0.010 4939
11700 -472.4050 0.010 4939
11800 -472.4050 0.010 4939
11900 -472.4046 0.010 4939
12000 -472.4045 0.010 4939
12100 -472.4045 0.010 4939
12200 -472.4044 0.010 4939
12300 -472.4044 0.010 4939
12400 -472.4043 0.010 4939
12500 -472.4040 0.010 4939
12600 -472.4040 0.010 4939
12700 -472.4040 0.010 4939
12800 -472.4038 0.010 4939
12900 -472.4038 0.010 4939
13000 -472.4037 0.010 4939
13100 -472.4035 0.010 4939
13200 -472.4033 0.010 4939
13300 -472.4033 0.010 4939
13400 -472.4032 0.010 4939
13500 -472.4031 0.010 4939
13600 -472.4031 0.010 4939
13700 -472.4029 0.010 4939
13800 -472.4029 0.010 4939
13900 -472.4029 0.010 4939
14000 -472.4028 0.010 4939
14100 -472.4026 0.010 4939
14200 -472.4024 0.010 4939
14300 -472.4024 0.010 4939
14400 -472.4024 0.010 4939
14500 -472.4023 0.010 4939
14600 -472.4023 0.010 4939
14700 -472.4023 0.010 4939
14800 -472.4023 0.010 4939
14900 -472.4021 0.010 4939
15000 -472.4020 0.010 4939
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
15100 -472.4020 0.010 4939
15200 -472.4020 0.010 4939
15300 -472.4020 0.010 4939
15400 -472.4020 0.010 4939
15500 -472.4019 0.010 4939
15600 -472.4019 0.010 4939
15700 -472.4019 0.010 4939
15800 -472.4019 0.010 4939
15900 -472.4017 0.010 4939
16000 -472.4017 0.010 4939
16100 -472.4016 0.010 4939
16200 -472.4015 0.010 4939
16300 -472.4013 0.010 4939
16400 -472.4013 0.010 4939
16500 -472.4012 0.010 4939
16600 -472.4012 0.010 4939
Reached termination condition!
last topological improvement at gen 4939
Improvement over last 500 gen = 0.00046
Current score = -472.4012
Performing final optimizations...
pass 1 : -472.4012 (branch= 0.0000)
pass 2 : -472.4012 (branch= 0.0000)
pass 3 : -472.3949 (branch= 0.0063)
pass 4 : -472.3918 (branch= 0.0031)
pass 5 : -472.3913 (branch= 0.0005)
pass 6 : -472.3912 (branch= 0.0002)
pass 7 : -472.3911 (branch= 0.0001)
pass 8 : -472.3910 (branch= 0.0001)
pass 9 : -472.3908 (branch= 0.0002)
pass 10: -472.3907 (branch= 0.0001)
pass 11: -472.3906 (branch= 0.0000)
pass 12: -472.3906 (branch= 0.0000)
pass 13: -472.3906 (branch= 0.0000)
Looking for minimum length branches...
Final score = -472.3906
Time used so far = 0 hours, 1 minutes and 34 seconds
MODEL REPORT - Parameter values are FINAL
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
7 branches were collapsed.
>>>Completed Search rep 2 (of 5)<<<
>>>Search rep 3 (of 5)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Starting with seed=1129809455
creating random starting tree...
Initial ln Likelihood: -1345.1873
optimizing: starting branch lengths...
pass 1:+ 462.206 (branch= 460.91 scale= 1.29)
pass 2:+ 46.315 (branch= 41.48 scale= 4.84)
pass 3:+ 8.901 (branch= 7.46 scale= 1.45)
pass 4:+ 0.399 (branch= 0.40 scale= 0.00)
lnL after optimization: -827.3663
gen current_lnL precision last_tree_imp
0 -827.3663 0.500 0
100 -554.0794 0.500 97
200 -519.0429 0.500 200
300 -495.8588 0.500 299
400 -491.6494 0.500 383
500 -489.6575 0.500 486
600 -485.5977 0.500 553
700 -484.4369 0.500 665
800 -483.6662 0.500 791
900 -483.1040 0.500 791
1000 -482.5508 0.500 947
1100 -481.4178 0.500 1088
1200 -479.8625 0.500 1193
1300 -478.7363 0.500 1277
1400 -477.3675 0.500 1379
1500 -476.5981 0.500 1469
1600 -476.2200 0.500 1469
1700 -475.8149 0.500 1469
1800 -475.6773 0.500 1469
1900 -475.5862 0.500 1892
2000 -475.0435 0.500 1953
2100 -474.6464 0.500 2047
2200 -474.5245 0.500 2047
2300 -474.2834 0.500 2047
2400 -474.1793 0.500 2047
2500 -474.0827 0.500 2047
2600 -474.0282 0.500 2047
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.003 lnL
2700 -473.8768 0.451 2047
2800 -473.8100 0.451 2047
2900 -473.7925 0.451 2047
3000 -473.7515 0.451 2963
3100 -473.6539 0.451 2963
3200 -473.6069 0.451 2963
3300 -473.5546 0.451 2963
3400 -473.4800 0.451 2963
3500 -473.4100 0.451 2963
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.017 lnL
3600 -473.3227 0.402 2963
3700 -473.2814 0.402 2963
3800 -473.2520 0.402 2963
3900 -473.2171 0.402 2963
4000 -473.1817 0.402 2963
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4100 -473.1732 0.353 2963
4200 -473.1482 0.353 2963
4300 -473.1308 0.353 2963
4400 -473.1219 0.353 2963
4500 -473.1118 0.353 2963
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4600 -473.1050 0.304 2963
4700 -473.1015 0.304 2963
4800 -473.0905 0.304 2963
4900 -473.0630 0.304 4831
5000 -473.0574 0.304 4831
5100 -473.0441 0.304 4831
5200 -473.0302 0.304 4831
5300 -473.0260 0.304 4831
5400 -473.0225 0.304 4831
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5500 -473.0122 0.255 4831
5600 -473.0074 0.255 4831
5700 -473.0044 0.255 4831
5800 -472.9855 0.255 5743
5900 -472.9802 0.255 5743
6000 -472.9770 0.255 5743
6100 -472.9697 0.255 5743
6200 -472.9691 0.255 5743
6300 -472.9684 0.255 5743
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
6400 -472.9103 0.206 6363
6500 -472.7831 0.206 6363
6600 -472.7122 0.206 6363
6700 -472.6699 0.206 6363
6800 -472.6517 0.206 6363
6900 -472.6270 0.206 6363
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
7000 -472.6085 0.157 6363
7100 -472.6020 0.157 6363
7200 -472.5927 0.157 6363
7300 -472.5865 0.157 6363
7400 -472.5660 0.157 6363
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.017 lnL
7500 -472.5448 0.108 6363
7600 -472.5350 0.108 6363
7700 -472.5283 0.108 6363
7800 -472.5265 0.108 6363
7900 -472.5211 0.108 6363
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
8000 -472.4754 0.059 7923
8100 -472.4617 0.059 7923
8200 -472.4586 0.059 7923
8300 -472.4552 0.059 7923
8400 -472.4521 0.059 7923
8500 -472.4492 0.059 7923
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.017 lnL
8600 -472.4288 0.010 7923
8700 -472.4266 0.010 7923
8800 -472.4230 0.010 7923
8900 -472.4226 0.010 7923
9000 -472.4214 0.010 7923
9100 -472.4198 0.010 7923
9200 -472.4185 0.010 7923
9300 -472.4181 0.010 7923
9400 -472.4177 0.010 7923
9500 -472.4175 0.010 7923
9600 -472.4173 0.010 7923
9700 -472.4160 0.010 7923
9800 -472.4160 0.010 7923
9900 -472.4160 0.010 7923
10000 -472.4155 0.010 7923
10100 -472.4152 0.010 7923
10200 -472.4148 0.010 7923
10300 -472.4145 0.010 7923
10400 -472.4140 0.010 7923
10500 -472.4138 0.010 7923
10600 -472.4138 0.010 7923
10700 -472.4137 0.010 7923
10800 -472.4132 0.010 7923
10900 -472.4130 0.010 7923
11000 -472.4125 0.010 7923
11100 -472.4124 0.010 7923
11200 -472.4123 0.010 7923
11300 -472.4121 0.010 7923
11400 -472.4121 0.010 7923
11500 -472.4118 0.010 7923
11600 -472.4115 0.010 7923
11700 -472.4114 0.010 7923
11800 -472.4114 0.010 7923
11900 -472.4114 0.010 7923
12000 -472.4112 0.010 7923
12100 -472.4108 0.010 7923
12200 -472.4106 0.010 7923
12300 -472.4106 0.010 7923
12400 -472.4102 0.010 7923
12500 -472.4102 0.010 7923
12600 -472.4101 0.010 7923
12700 -472.4100 0.010 7923
12800 -472.4100 0.010 7923
12900 -472.4100 0.010 7923
13000 -472.4099 0.010 7923
13100 -472.4096 0.010 7923
13200 -472.4094 0.010 7923
13300 -472.4094 0.010 7923
13400 -472.4092 0.010 7923
13500 -472.4091 0.010 7923
13600 -472.4088 0.010 7923
13700 -472.4086 0.010 7923
13800 -472.4086 0.010 7923
13900 -472.4084 0.010 7923
14000 -472.4084 0.010 7923
14100 -472.4083 0.010 7923
14200 -472.4081 0.010 7923
14300 -472.4081 0.010 7923
14400 -472.4076 0.010 7923
14500 -472.4075 0.010 7923
14600 -472.4074 0.010 7923
14700 -472.4073 0.010 7923
14800 -472.4073 0.010 7923
14900 -472.4073 0.010 7923
15000 -472.4072 0.010 7923
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
15100 -472.4072 0.010 7923
15200 -472.4070 0.010 7923
15300 -472.4070 0.010 7923
15400 -472.4069 0.010 7923
15500 -472.4067 0.010 7923
15600 -472.4066 0.010 7923
15700 -472.4066 0.010 7923
15800 -472.4065 0.010 7923
15900 -472.4064 0.010 7923
16000 -472.4064 0.010 7923
16100 -472.4063 0.010 7923
16200 -472.4063 0.010 7923
16300 -472.4063 0.010 7923
16400 -472.4062 0.010 7923
16500 -472.4061 0.010 7923
16600 -472.4061 0.010 7923
16700 -472.4061 0.010 7923
16800 -472.4061 0.010 7923
16900 -472.4061 0.010 7923
17000 -472.4060 0.010 7923
17100 -472.4058 0.010 7923
17200 -472.4058 0.010 7923
17300 -472.4058 0.010 7923
17400 -472.4058 0.010 7923
17500 -472.4057 0.010 7923
17600 -472.4057 0.010 7923
17700 -472.4055 0.010 7923
17800 -472.4055 0.010 7923
17900 -472.4052 0.010 7923
18000 -472.4048 0.010 7923
18100 -472.4048 0.010 7923
18200 -472.4048 0.010 7923
18300 -472.4047 0.010 7923
18400 -472.4047 0.010 7923
18500 -472.4046 0.010 7923
18600 -472.4046 0.010 7923
Reached termination condition!
last topological improvement at gen 7923
Improvement over last 500 gen = 0.00024
Current score = -472.4046
Performing final optimizations...
pass 1 : -472.4046 (branch= 0.0000)
pass 2 : -472.4046 (branch= 0.0000)
pass 3 : -472.3930 (branch= 0.0116)
pass 4 : -472.3918 (branch= 0.0012)
pass 5 : -472.3912 (branch= 0.0006)
pass 6 : -472.3912 (branch= 0.0000)
pass 7 : -472.3910 (branch= 0.0002)
pass 8 : -472.3909 (branch= 0.0001)
pass 9 : -472.3908 (branch= 0.0001)
pass 10: -472.3907 (branch= 0.0001)
pass 11: -472.3906 (branch= 0.0001)
pass 12: -472.3906 (branch= 0.0000)
pass 13: -472.3906 (branch= 0.0000)
pass 14: -472.3906 (branch= 0.0000)
Looking for minimum length branches...
Final score = -472.3906
Time used so far = 0 hours, 2 minutes and 22 seconds
MODEL REPORT - Parameter values are FINAL
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
7 branches were collapsed.
>>>Completed Search rep 3 (of 5)<<<
>>>Search rep 4 (of 5)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Starting with seed=1786917786
creating random starting tree...
Initial ln Likelihood: -1259.6816
optimizing: starting branch lengths...
pass 1:+ 411.545 (branch= 410.14 scale= 1.40)
pass 2:+ 34.424 (branch= 31.96 scale= 2.47)
pass 3:+ 4.884 (branch= 4.25 scale= 0.63)
pass 4:+ 1.721 (branch= 1.72 scale= 0.00)
pass 5:+ 0.047 (branch= 0.05 scale= 0.00)
lnL after optimization: -807.0589
gen current_lnL precision last_tree_imp
0 -807.0589 0.500 0
100 -601.5939 0.500 100
200 -526.3617 0.500 196
300 -512.4135 0.500 278
400 -483.5238 0.500 390
500 -481.4931 0.500 471
600 -481.0061 0.500 471
700 -480.0821 0.500 683
800 -477.5502 0.500 729
900 -477.1062 0.500 729
1000 -476.7058 0.500 729
1100 -476.2214 0.500 729
1200 -475.8903 0.500 729
1300 -475.6326 0.500 1292
1400 -475.4871 0.500 1292
1500 -475.3881 0.500 1292
1600 -475.1881 0.500 1598
1700 -474.9285 0.500 1598
1800 -474.7453 0.500 1598
1900 -474.6094 0.500 1887
2000 -474.5233 0.500 1887
2100 -474.4728 0.500 2088
2200 -474.4253 0.500 2088
2300 -474.3405 0.500 2088
2400 -474.2962 0.500 2088
2500 -474.2187 0.500 2088
2600 -474.1912 0.500 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.001 lnL
2700 -474.1788 0.451 2088
2800 -474.1712 0.451 2088
2900 -474.1538 0.451 2088
3000 -474.1458 0.451 2088
3100 -474.1336 0.451 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.001 lnL
3200 -474.1318 0.402 2088
3300 -474.1252 0.402 2088
3400 -474.1154 0.402 2088
3500 -474.1050 0.402 2088
3600 -474.0923 0.402 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3700 -474.0853 0.353 2088
3800 -474.0781 0.353 2088
3900 -474.0710 0.353 2088
4000 -474.0676 0.353 2088
4100 -474.0557 0.353 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4200 -474.0534 0.304 2088
4300 -474.0477 0.304 2088
4400 -474.0391 0.304 2088
4500 -474.0353 0.304 2088
4600 -474.0334 0.304 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4700 -474.0283 0.255 2088
4800 -474.0282 0.255 2088
4900 -474.0262 0.255 2088
5000 -474.0228 0.255 2088
5100 -474.0183 0.255 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5200 -474.0155 0.206 2088
5300 -474.0118 0.206 2088
5400 -474.0089 0.206 2088
5500 -474.0077 0.206 2088
5600 -474.0053 0.206 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5700 -474.0043 0.157 2088
5800 -474.0024 0.157 2088
5900 -474.0009 0.157 2088
6000 -474.0001 0.157 2088
6100 -473.9987 0.157 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
6200 -473.9969 0.108 2088
6300 -473.9937 0.108 2088
6400 -473.9927 0.108 2088
6500 -473.9916 0.108 2088
6600 -473.9905 0.108 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
6700 -473.9882 0.059 2088
6800 -473.9871 0.059 2088
6900 -473.9863 0.059 2088
7000 -473.9859 0.059 2088
7100 -473.9843 0.059 2088
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.042 lnL
7200 -473.9424 0.010 2088
7300 -473.9419 0.010 2088
7400 -473.9416 0.010 2088
7500 -473.9414 0.010 2088
7600 -473.9411 0.010 2088
7700 -473.9398 0.010 2088
7800 -473.9393 0.010 2088
7900 -473.9384 0.010 2088
8000 -473.9377 0.010 2088
8100 -473.9376 0.010 2088
8200 -473.9352 0.010 2088
8300 -473.9337 0.010 2088
8400 -473.9331 0.010 2088
8500 -473.9321 0.010 2088
8600 -473.9303 0.010 2088
8700 -473.8109 0.010 8647
8800 -473.7338 0.010 8717
8900 -473.6620 0.010 8717
9000 -473.6447 0.010 8717
9100 -473.6360 0.010 8717
9200 -473.6289 0.010 8717
9300 -473.6274 0.010 8717
9400 -473.6244 0.010 8717
9500 -473.6190 0.010 8717
9600 -473.6187 0.010 8717
9700 -473.6164 0.010 8717
9800 -473.6158 0.010 8717
9900 -473.6154 0.010 8717
10000 -473.6148 0.010 8717
10100 -473.6148 0.010 8717
10200 -473.6146 0.010 8717
10300 -473.6141 0.010 8717
10400 -473.6141 0.010 8717
10500 -473.6139 0.010 8717
10600 -473.6138 0.010 8717
10700 -473.6136 0.010 8717
10800 -473.6134 0.010 8717
10900 -473.6134 0.010 8717
11000 -473.6132 0.010 8717
11100 -473.6132 0.010 8717
11200 -473.6130 0.010 8717
11300 -473.6129 0.010 8717
11400 -473.6129 0.010 8717
11500 -473.6128 0.010 8717
11600 -473.6128 0.010 8717
11700 -473.6126 0.010 8717
11800 -473.6124 0.010 8717
11900 -473.6124 0.010 8717
12000 -473.6122 0.010 8717
12100 -473.6122 0.010 8717
12200 -473.6122 0.010 8717
12300 -473.6122 0.010 8717
12400 -473.6121 0.010 8717
12500 -473.6120 0.010 8717
12600 -473.6119 0.010 8717
12700 -473.6119 0.010 8717
12800 -473.6119 0.010 8717
12900 -473.6118 0.010 8717
13000 -473.6118 0.010 8717
13100 -473.6118 0.010 8717
13200 -473.6117 0.010 8717
13300 -473.6116 0.010 8717
13400 -473.6116 0.010 8717
13500 -473.6115 0.010 8717
13600 -473.6113 0.010 8717
13700 -473.6113 0.010 8717
13800 -473.6113 0.010 8717
13900 -473.6112 0.010 8717
14000 -473.6112 0.010 8717
14100 -473.6112 0.010 8717
14200 -473.6112 0.010 8717
14300 -473.6109 0.010 8717
14400 -473.6108 0.010 8717
14500 -473.6107 0.010 8717
14600 -473.6106 0.010 8717
14700 -473.6106 0.010 8717
14800 -473.6106 0.010 8717
14900 -473.6105 0.010 8717
15000 -473.6105 0.010 8717
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
15100 -473.6104 0.010 8717
15200 -473.6104 0.010 8717
15300 -473.6101 0.010 8717
15400 -473.6101 0.010 8717
15500 -473.6100 0.010 8717
15600 -473.6100 0.010 8717
15700 -473.6099 0.010 8717
15800 -473.6098 0.010 8717
15900 -473.6098 0.010 8717
16000 -473.6098 0.010 8717
16100 -473.6098 0.010 8717
16200 -473.6098 0.010 8717
16300 -473.6097 0.010 8717
16400 -473.6097 0.010 8717
16500 -473.6097 0.010 8717
16600 -473.6096 0.010 8717
16700 -473.6096 0.010 8717
16800 -473.6095 0.010 8717
16900 -473.6094 0.010 8717
17000 -473.6093 0.010 8717
17100 -473.6093 0.010 8717
17200 -473.6092 0.010 8717
17300 -473.6091 0.010 8717
17400 -473.6091 0.010 8717
17500 -473.6090 0.010 8717
17600 -473.6089 0.010 8717
17700 -473.6089 0.010 8717
17800 -473.6089 0.010 8717
17900 -473.6088 0.010 8717
18000 -473.6088 0.010 8717
18100 -473.6088 0.010 8717
18200 -473.6087 0.010 8717
18300 -473.6087 0.010 8717
18400 -473.6086 0.010 8717
18500 -473.6086 0.010 8717
18600 -473.6084 0.010 8717
18700 -473.6084 0.010 8717
18800 -473.6084 0.010 8717
Reached termination condition!
last topological improvement at gen 8717
Improvement over last 500 gen = 0.00033
Current score = -473.6084
Performing final optimizations...
pass 1 : -473.6084 (branch= 0.0000)
pass 2 : -473.6084 (branch= 0.0000)
pass 3 : -473.5997 (branch= 0.0087)
pass 4 : -473.5967 (branch= 0.0030)
pass 5 : -473.5967 (branch= 0.0000)
pass 6 : -473.5967 (branch= 0.0000)
pass 7 : -473.5967 (branch= 0.0000)
pass 8 : -473.5966 (branch= 0.0001)
pass 9 : -473.5966 (branch= 0.0001)
pass 10: -473.5964 (branch= 0.0001)
pass 11: -473.5964 (branch= 0.0001)
pass 12: -473.5964 (branch= 0.0000)
Looking for minimum length branches...
Final score = -473.5964
Time used so far = 0 hours, 3 minutes and 11 seconds
MODEL REPORT - Parameter values are FINAL
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
7 branches were collapsed.
>>>Completed Search rep 4 (of 5)<<<
>>>Search rep 5 (of 5)<<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Starting with seed=1429655032
creating random starting tree...
Initial ln Likelihood: -1219.3334
optimizing: starting branch lengths...
pass 1:+ 350.904 (branch= 350.90 scale= 0.00)
pass 2:+ 56.702 (branch= 53.13 scale= 3.58)
pass 3:+ 20.452 (branch= 17.31 scale= 3.14)
pass 4:+ 3.274 (branch= 2.54 scale= 0.73)
pass 5:+ 2.093 (branch= 1.31 scale= 0.78)
pass 6:+ 1.698 (branch= 1.70 scale= 0.00)
pass 7:+ 0.095 (branch= 0.09 scale= 0.00)
lnL after optimization: -784.1160
gen current_lnL precision last_tree_imp
0 -784.1160 0.500 0
100 -593.8019 0.500 100
200 -533.4957 0.500 192
300 -516.5071 0.500 287
400 -508.1399 0.500 397
500 -489.8206 0.500 499
600 -483.5815 0.500 564
700 -480.9720 0.500 670
800 -480.2684 0.500 773
900 -479.5095 0.500 773
1000 -479.1002 0.500 773
1100 -478.7379 0.500 773
1200 -478.3594 0.500 773
1300 -477.9320 0.500 773
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.244 lnL
1400 -477.3303 0.451 773
1500 -476.9782 0.451 1469
1600 -476.6121 0.451 1469
1700 -476.4869 0.451 1469
1800 -476.4165 0.451 1469
1900 -476.2181 0.451 1469
2000 -476.1044 0.451 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.001 lnL
2100 -475.8182 0.402 1469
2200 -475.6823 0.402 1469
2300 -475.5295 0.402 1469
2400 -475.4160 0.402 1469
2500 -475.3457 0.402 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.002 lnL
2600 -475.3139 0.353 1469
2700 -475.2752 0.353 1469
2800 -475.2199 0.353 1469
2900 -475.1825 0.353 1469
3000 -475.1627 0.353 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3100 -475.1412 0.304 1469
3200 -475.1168 0.304 1469
3300 -475.0961 0.304 1469
3400 -475.0782 0.304 1469
3500 -475.0663 0.304 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
3600 -475.0616 0.255 1469
3700 -474.8098 0.255 1469
3800 -474.7550 0.255 1469
3900 -474.7510 0.255 1469
4000 -474.7427 0.255 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4100 -474.7305 0.206 1469
4200 -474.7217 0.206 1469
4300 -474.7104 0.206 1469
4400 -474.7037 0.206 1469
4500 -474.7028 0.206 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
4600 -474.7019 0.157 1469
4700 -474.6963 0.157 1469
4800 -474.6919 0.157 1469
4900 -474.6899 0.157 1469
5000 -474.6870 0.157 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5100 -474.6848 0.108 1469
5200 -474.6823 0.108 1469
5300 -474.6807 0.108 1469
5400 -474.6786 0.108 1469
5500 -474.6774 0.108 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
5600 -474.6750 0.059 1469
5700 -474.6731 0.059 1469
5800 -474.6718 0.059 1469
5900 -474.6693 0.059 1469
6000 -474.6675 0.059 1469
Optimization precision reduced
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.043 lnL
6100 -474.6238 0.010 1469
6200 -474.6194 0.010 1469
6300 -474.6183 0.010 1469
6400 -474.6182 0.010 1469
6500 -474.6179 0.010 1469
6600 -474.6176 0.010 1469
6700 -474.6174 0.010 1469
6800 -474.6173 0.010 1469
6900 -474.6170 0.010 1469
7000 -474.6139 0.010 1469
7100 -474.6139 0.010 1469
7200 -474.6136 0.010 1469
7300 -474.6131 0.010 1469
7400 -474.6126 0.010 1469
7500 -474.6123 0.010 1469
7600 -474.6120 0.010 1469
7700 -474.6117 0.010 1469
7800 -474.6116 0.010 1469
7900 -474.6115 0.010 1469
8000 -474.6113 0.010 1469
8100 -474.6108 0.010 1469
8200 -474.6105 0.010 1469
8300 -474.6100 0.010 1469
8400 -474.6099 0.010 1469
8500 -474.6092 0.010 1469
8600 -474.6088 0.010 1469
8700 -474.6088 0.010 1469
8800 -474.6086 0.010 1469
8900 -474.6084 0.010 1469
9000 -474.6081 0.010 1469
9100 -474.6079 0.010 1469
9200 -474.6076 0.010 1469
9300 -474.6076 0.010 1469
9400 -474.6076 0.010 1469
9500 -474.6072 0.010 1469
9600 -474.6070 0.010 1469
9700 -474.6067 0.010 1469
9800 -474.6067 0.010 1469
9900 -474.6065 0.010 1469
10000 -474.6064 0.010 1469
10100 -474.6064 0.010 1469
10200 -474.6062 0.010 1469
10300 -474.6062 0.010 1469
10400 -474.6062 0.010 1469
10500 -474.6062 0.010 1469
10600 -474.6061 0.010 1469
10700 -474.6061 0.010 1469
10800 -474.6061 0.010 1469
10900 -474.6060 0.010 1469
11000 -474.6060 0.010 1469
11100 -474.6060 0.010 1469
11200 -474.6060 0.010 1469
11300 -474.6060 0.010 1469
11400 -474.6059 0.010 1469
11500 -474.6058 0.010 1469
11600 -474.6057 0.010 1469
11700 -474.6057 0.010 1469
11800 -474.6057 0.010 1469
11900 -474.6057 0.010 1469
12000 -474.6056 0.010 1469
12100 -474.6056 0.010 1469
12200 -474.6056 0.010 1469
12300 -474.6055 0.010 1469
12400 -474.6055 0.010 1469
12500 -474.6055 0.010 1469
12600 -474.6055 0.010 1469
12700 -474.6055 0.010 1469
12800 -474.6054 0.010 1469
12900 -474.6054 0.010 1469
13000 -474.6052 0.010 1469
13100 -474.6050 0.010 1469
13200 -474.6050 0.010 1469
13300 -474.6049 0.010 1469
13400 -474.6048 0.010 1469
13500 -474.6048 0.010 1469
13600 -474.6046 0.010 1469
13700 -474.6042 0.010 1469
13800 -474.6040 0.010 1469
13900 -474.6040 0.010 1469
14000 -474.6039 0.010 1469
14100 -474.6039 0.010 1469
14200 -474.6039 0.010 1469
14300 -474.6038 0.010 1469
14400 -474.6035 0.010 1469
14500 -474.6034 0.010 1469
14600 -474.6033 0.010 1469
14700 -474.6032 0.010 1469
14800 -474.6030 0.010 1469
14900 -474.6030 0.010 1469
15000 -474.6028 0.010 1469
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.000 lnL
15100 -474.6028 0.010 1469
15200 -474.6028 0.010 1469
15300 -474.6027 0.010 1469
15400 -474.6027 0.010 1469
15500 -474.6027 0.010 1469
15600 -474.6026 0.010 1469
15700 -474.6025 0.010 1469
15800 -474.6024 0.010 1469
15900 -474.6024 0.010 1469
16000 -474.6023 0.010 1469
16100 -474.6022 0.010 1469
Reached termination condition!
last topological improvement at gen 1469
Improvement over last 500 gen = 0.00041
Current score = -474.6022
Performing final optimizations...
pass 1 : -474.6022 (branch= 0.0000)
pass 2 : -474.5995 (branch= 0.0027)
pass 3 : -474.5871 (branch= 0.0124)
pass 4 : -474.5871 (branch= 0.0000)
pass 5 : -474.5868 (branch= 0.0003)
pass 6 : -474.5866 (branch= 0.0001)
pass 7 : -474.5864 (branch= 0.0002)
pass 8 : -474.5862 (branch= 0.0002)
pass 9 : -474.5861 (branch= 0.0002)
pass 10: -474.5860 (branch= 0.0000)
pass 11: -474.5860 (branch= 0.0000)
pass 12: -474.5860 (branch= 0.0000)
pass 13: -474.5860 (branch= 0.0000)
Looking for minimum length branches...
Final score = -474.5860
Time used = 0 hours, 3 minutes and 54 seconds
MODEL REPORT - Parameter values are FINAL
Model 1
Number of states = 2 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.50, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 2
Number of states = 3 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.33, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
Model 3
Number of states = 4 (standard data)
Character change matrix:
One rate (symmetric one rate Mkv model)
Equilibrium State Frequencies: equal (0.25, fixed)
Rate Heterogeneity Model:
no rate heterogeneity
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
7 branches were collapsed.
>>>Completed Search rep 5 (of 5)<<<
#######################################################
Completed 5 replicate search(es) (of 5).
NOTE: Unless the following output indicates that search replicates found the
same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -472.3908
Replicate 2 : -472.3906
Replicate 3 : -472.3906 (best) (same topology as 2)
Replicate 4 : -473.5964
Replicate 5 : -474.5860
Parameter estimates across search replicates:
Partition model subset 1:
Model contains no estimated parameters
Partition model subset 2:
Model contains no estimated parameters
Partition model subset 3:
Model contains no estimated parameters
Treelengths:
TL
rep 1: 3.623
rep 2: 3.622
rep 3: 3.621
rep 4: 3.807
rep 5: 3.572
Saving final trees from all search reps to mkv.best.all.tre
Saving final tree from best search rep (#3) to mkv.best.tre
#######################################################
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