IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_99_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_A_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_132_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_133_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_131_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_130_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_130_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_60aa-ORF_renamed_min100aa_ORF are exactly identical

IMPORTANT WARNING
Found 6 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.

Just in case you might need it, an alignment file with 
sequence duplicates removed is printed to file Ymf83.renamed.muscle.Oligohymenophorea.fa.reduced


This is RAxML version 8.1.3 released by Alexandros Stamatakis on August 13 2014.

With greatly appreciated code contributions by:
Andre Aberer      (HITS)
Simon Berger      (HITS)
Alexey Kozlov     (HITS)
Kassian Kobert    (HITS)
David Dao         (KIT and HITS)
Nick Pattengale   (Sandia)
Wayne Pfeiffer    (SDSC)
Akifumi S. Tanabe (NRIFS)

Alignment has 171 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 27.86%

RAxML rapid bootstrapping and subsequent ML search

Using 1 distinct models/data partitions with joint branch length optimization



Executing 100 rapid bootstrap inferences and thereafter a thorough ML search 

All free model parameters will be estimated by RAxML
GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 171
Name: No Name Provided
DataType: AA
Substitution Matrix: GTR
Using empirical base frequencies




RAxML was called as follows:

raxml -f a -s Ymf83.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 



Printed linked AA GTR matrix that achieved an overall improvement of 92.112807 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 7.801749 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.550924 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Time for BS model parameter optimization 11.384425
Bootstrap[0]: Time 12.185949 seconds, bootstrap likelihood -2100.739708, best rearrangement setting 13
Bootstrap[1]: Time 0.659549 seconds, bootstrap likelihood -1899.425490, best rearrangement setting 13
Bootstrap[2]: Time 0.793575 seconds, bootstrap likelihood -2154.445155, best rearrangement setting 12
Bootstrap[3]: Time 0.720728 seconds, bootstrap likelihood -2056.942778, best rearrangement setting 15
Bootstrap[4]: Time 0.702327 seconds, bootstrap likelihood -2149.827749, best rearrangement setting 10
Bootstrap[5]: Time 0.677201 seconds, bootstrap likelihood -2056.022986, best rearrangement setting 10
Bootstrap[6]: Time 0.676012 seconds, bootstrap likelihood -1989.666715, best rearrangement setting 6
Bootstrap[7]: Time 0.610378 seconds, bootstrap likelihood -1977.073032, best rearrangement setting 14
Bootstrap[8]: Time 0.706350 seconds, bootstrap likelihood -1921.415379, best rearrangement setting 5
Bootstrap[9]: Time 0.681675 seconds, bootstrap likelihood -2064.081239, best rearrangement setting 7
Bootstrap[10]: Time 0.663250 seconds, bootstrap likelihood -2104.461095, best rearrangement setting 7
Bootstrap[11]: Time 0.699420 seconds, bootstrap likelihood -2026.318913, best rearrangement setting 5
Bootstrap[12]: Time 0.804059 seconds, bootstrap likelihood -2140.288704, best rearrangement setting 8
Bootstrap[13]: Time 0.709933 seconds, bootstrap likelihood -1927.207816, best rearrangement setting 7
Bootstrap[14]: Time 0.582386 seconds, bootstrap likelihood -1931.430574, best rearrangement setting 12
Bootstrap[15]: Time 0.707116 seconds, bootstrap likelihood -2052.062090, best rearrangement setting 15
Bootstrap[16]: Time 0.652831 seconds, bootstrap likelihood -2015.057354, best rearrangement setting 12
Bootstrap[17]: Time 0.633273 seconds, bootstrap likelihood -1987.196670, best rearrangement setting 12
Bootstrap[18]: Time 0.699080 seconds, bootstrap likelihood -2149.693961, best rearrangement setting 5
Bootstrap[19]: Time 0.723604 seconds, bootstrap likelihood -2052.050548, best rearrangement setting 8
Bootstrap[20]: Time 0.761179 seconds, bootstrap likelihood -2030.606165, best rearrangement setting 10
Bootstrap[21]: Time 0.578470 seconds, bootstrap likelihood -1991.136316, best rearrangement setting 6
Bootstrap[22]: Time 0.617715 seconds, bootstrap likelihood -2100.697421, best rearrangement setting 5
Bootstrap[23]: Time 0.251546 seconds, bootstrap likelihood -2215.764021, best rearrangement setting 7
Bootstrap[24]: Time 0.672443 seconds, bootstrap likelihood -2048.389644, best rearrangement setting 8
Bootstrap[25]: Time 0.796389 seconds, bootstrap likelihood -1989.703556, best rearrangement setting 6
Bootstrap[26]: Time 0.654435 seconds, bootstrap likelihood -2039.795348, best rearrangement setting 12
Bootstrap[27]: Time 0.630677 seconds, bootstrap likelihood -2006.812613, best rearrangement setting 10
Bootstrap[28]: Time 0.684500 seconds, bootstrap likelihood -2064.650979, best rearrangement setting 11
Bootstrap[29]: Time 0.749649 seconds, bootstrap likelihood -2149.542567, best rearrangement setting 12
Bootstrap[30]: Time 0.561961 seconds, bootstrap likelihood -2048.445653, best rearrangement setting 15
Bootstrap[31]: Time 0.713739 seconds, bootstrap likelihood -1895.401270, best rearrangement setting 15
Bootstrap[32]: Time 0.239937 seconds, bootstrap likelihood -2077.937165, best rearrangement setting 6
Bootstrap[33]: Time 0.659991 seconds, bootstrap likelihood -2055.510247, best rearrangement setting 15
Bootstrap[34]: Time 0.718833 seconds, bootstrap likelihood -2091.194599, best rearrangement setting 11
Bootstrap[35]: Time 0.244807 seconds, bootstrap likelihood -1925.415812, best rearrangement setting 8
Bootstrap[36]: Time 0.637696 seconds, bootstrap likelihood -1960.533729, best rearrangement setting 9
Bootstrap[37]: Time 0.596688 seconds, bootstrap likelihood -1990.343203, best rearrangement setting 11
Bootstrap[38]: Time 0.234455 seconds, bootstrap likelihood -2135.869020, best rearrangement setting 8
Bootstrap[39]: Time 0.643977 seconds, bootstrap likelihood -1991.683041, best rearrangement setting 13
Bootstrap[40]: Time 0.748284 seconds, bootstrap likelihood -2152.582331, best rearrangement setting 13
Bootstrap[41]: Time 0.245496 seconds, bootstrap likelihood -2143.782124, best rearrangement setting 10
Bootstrap[42]: Time 0.750238 seconds, bootstrap likelihood -1962.094820, best rearrangement setting 5
Bootstrap[43]: Time 0.291633 seconds, bootstrap likelihood -2054.451065, best rearrangement setting 14
Bootstrap[44]: Time 0.296430 seconds, bootstrap likelihood -2021.656985, best rearrangement setting 10
Bootstrap[45]: Time 0.625059 seconds, bootstrap likelihood -1979.714986, best rearrangement setting 15
Bootstrap[46]: Time 0.632358 seconds, bootstrap likelihood -1969.415082, best rearrangement setting 14
Bootstrap[47]: Time 0.688090 seconds, bootstrap likelihood -2118.943462, best rearrangement setting 8
Bootstrap[48]: Time 0.573260 seconds, bootstrap likelihood -1841.059174, best rearrangement setting 6
Bootstrap[49]: Time 0.680324 seconds, bootstrap likelihood -2091.627893, best rearrangement setting 7
Bootstrap[50]: Time 0.679746 seconds, bootstrap likelihood -2104.514190, best rearrangement setting 7
Bootstrap[51]: Time 0.587413 seconds, bootstrap likelihood -1975.883824, best rearrangement setting 11
Bootstrap[52]: Time 0.658615 seconds, bootstrap likelihood -2139.767157, best rearrangement setting 12
Bootstrap[53]: Time 0.656288 seconds, bootstrap likelihood -2074.455323, best rearrangement setting 8
Bootstrap[54]: Time 0.744610 seconds, bootstrap likelihood -2101.030040, best rearrangement setting 9
Bootstrap[55]: Time 0.654890 seconds, bootstrap likelihood -1859.760953, best rearrangement setting 11
Bootstrap[56]: Time 0.597836 seconds, bootstrap likelihood -2021.865151, best rearrangement setting 5
Bootstrap[57]: Time 0.671309 seconds, bootstrap likelihood -1977.196291, best rearrangement setting 7
Bootstrap[58]: Time 0.630871 seconds, bootstrap likelihood -2038.254655, best rearrangement setting 10
Bootstrap[59]: Time 0.649294 seconds, bootstrap likelihood -2218.568619, best rearrangement setting 9
Bootstrap[60]: Time 0.712643 seconds, bootstrap likelihood -2073.635221, best rearrangement setting 7
Bootstrap[61]: Time 0.633563 seconds, bootstrap likelihood -2161.684402, best rearrangement setting 5
Bootstrap[62]: Time 0.722329 seconds, bootstrap likelihood -2145.269801, best rearrangement setting 11
Bootstrap[63]: Time 0.724323 seconds, bootstrap likelihood -2015.052579, best rearrangement setting 12
Bootstrap[64]: Time 0.648684 seconds, bootstrap likelihood -1944.474012, best rearrangement setting 7
Bootstrap[65]: Time 0.781092 seconds, bootstrap likelihood -1939.201487, best rearrangement setting 5
Bootstrap[66]: Time 0.733760 seconds, bootstrap likelihood -2043.730854, best rearrangement setting 5
Bootstrap[67]: Time 0.770492 seconds, bootstrap likelihood -2038.122993, best rearrangement setting 15
Bootstrap[68]: Time 0.575558 seconds, bootstrap likelihood -1955.860486, best rearrangement setting 11
Bootstrap[69]: Time 0.611411 seconds, bootstrap likelihood -1885.282491, best rearrangement setting 5
Bootstrap[70]: Time 0.737572 seconds, bootstrap likelihood -2046.856777, best rearrangement setting 8
Bootstrap[71]: Time 0.735935 seconds, bootstrap likelihood -1815.397567, best rearrangement setting 10
Bootstrap[72]: Time 0.764136 seconds, bootstrap likelihood -2123.081484, best rearrangement setting 11
Bootstrap[73]: Time 0.662237 seconds, bootstrap likelihood -1962.574157, best rearrangement setting 9
Bootstrap[74]: Time 0.623724 seconds, bootstrap likelihood -2232.022344, best rearrangement setting 5
Bootstrap[75]: Time 0.545099 seconds, bootstrap likelihood -1928.873423, best rearrangement setting 8
Bootstrap[76]: Time 0.718197 seconds, bootstrap likelihood -1930.005393, best rearrangement setting 9
Bootstrap[77]: Time 0.689733 seconds, bootstrap likelihood -1986.795377, best rearrangement setting 11
Bootstrap[78]: Time 0.676108 seconds, bootstrap likelihood -2081.787141, best rearrangement setting 15
Bootstrap[79]: Time 0.682232 seconds, bootstrap likelihood -1908.419405, best rearrangement setting 9
Bootstrap[80]: Time 0.817343 seconds, bootstrap likelihood -2016.262790, best rearrangement setting 15
Bootstrap[81]: Time 0.653161 seconds, bootstrap likelihood -1872.365767, best rearrangement setting 7
Bootstrap[82]: Time 0.633771 seconds, bootstrap likelihood -2032.354071, best rearrangement setting 6
Bootstrap[83]: Time 0.624692 seconds, bootstrap likelihood -2088.272082, best rearrangement setting 10
Bootstrap[84]: Time 0.259347 seconds, bootstrap likelihood -2142.475210, best rearrangement setting 11
Bootstrap[85]: Time 0.699776 seconds, bootstrap likelihood -2047.368794, best rearrangement setting 8
Bootstrap[86]: Time 0.728685 seconds, bootstrap likelihood -2134.204708, best rearrangement setting 7
Bootstrap[87]: Time 0.717022 seconds, bootstrap likelihood -1927.096132, best rearrangement setting 7
Bootstrap[88]: Time 0.796778 seconds, bootstrap likelihood -2254.915852, best rearrangement setting 12
Bootstrap[89]: Time 0.225711 seconds, bootstrap likelihood -2100.400986, best rearrangement setting 10
Bootstrap[90]: Time 0.771371 seconds, bootstrap likelihood -2259.470522, best rearrangement setting 8
Bootstrap[91]: Time 0.724619 seconds, bootstrap likelihood -2164.608300, best rearrangement setting 12
Bootstrap[92]: Time 0.709133 seconds, bootstrap likelihood -2052.693450, best rearrangement setting 13
Bootstrap[93]: Time 0.608513 seconds, bootstrap likelihood -2054.490164, best rearrangement setting 15
Bootstrap[94]: Time 0.676820 seconds, bootstrap likelihood -1985.854537, best rearrangement setting 5
Bootstrap[95]: Time 0.681054 seconds, bootstrap likelihood -2109.149752, best rearrangement setting 5
Bootstrap[96]: Time 0.701141 seconds, bootstrap likelihood -2058.045917, best rearrangement setting 13
Bootstrap[97]: Time 0.727441 seconds, bootstrap likelihood -2006.275400, best rearrangement setting 11
Bootstrap[98]: Time 0.301871 seconds, bootstrap likelihood -1878.523838, best rearrangement setting 6
Bootstrap[99]: Time 0.734009 seconds, bootstrap likelihood -2235.163902, best rearrangement setting 14


Overall Time for 100 Rapid Bootstraps 75.619134 seconds
Average Time per Rapid Bootstrap 0.756191 seconds

Starting ML Search ...


Printed linked AA GTR matrix that achieved an overall improvement of 94.948625 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 8.270250 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.405014 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.175920 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.046943 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Fast ML optimization finished

Fast ML search Time: 51.010323 seconds


Printed linked AA GTR matrix that achieved an overall improvement of 93.053133 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 7.982851 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.544638 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.133538 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.043345 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Slow ML Search 0 Likelihood: -2051.303738
Slow ML Search 1 Likelihood: -2051.303738
Slow ML Search 2 Likelihood: -2051.303740
Slow ML Search 3 Likelihood: -2051.303743
Slow ML Search 4 Likelihood: -2051.303743
Slow ML Search 5 Likelihood: -2051.303743
Slow ML Search 6 Likelihood: -2051.303743
Slow ML Search 7 Likelihood: -2051.303743
Slow ML Search 8 Likelihood: -2051.303743
Slow ML Search 9 Likelihood: -2051.303743
Slow ML optimization finished

Slow ML search Time: 32.129625 seconds

Printed linked AA GTR matrix that achieved an overall improvement of 93.087085 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 7.950330 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.543354 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.133305 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.043233 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Thorough ML search Time: 19.479043 seconds

Final ML Optimization Likelihood: -2051.303883

Model Information:

Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha: 1.129544
Tree-Length: 2.877958
rate A <-> R: 0.000000
rate A <-> N: 0.000000
rate A <-> D: 0.000000
rate A <-> C: 3.857536
rate A <-> Q: 0.000000
rate A <-> E: 3.137088
rate A <-> G: 57.480950
rate A <-> H: 0.000000
rate A <-> I: 5.161040
rate A <-> L: 0.000000
rate A <-> K: 0.000000
rate A <-> M: 0.000000
rate A <-> F: 2.428623
rate A <-> P: 5.897390
rate A <-> S: 9.810497
rate A <-> T: 11.438385
rate A <-> W: 0.000000
rate A <-> Y: 0.000000
rate A <-> V: 22.117077
rate R <-> N: 4.547412
rate R <-> D: 0.000000
rate R <-> C: 4.927546
rate R <-> Q: 0.000000
rate R <-> E: 0.000000
rate R <-> G: 0.000000
rate R <-> H: 0.000000
rate R <-> I: 1.159235
rate R <-> L: 0.000000
rate R <-> K: 11.440882
rate R <-> M: 0.000000
rate R <-> F: 0.000000
rate R <-> P: 0.000000
rate R <-> S: 6.729420
rate R <-> T: 0.000000
rate R <-> W: 0.000000
rate R <-> Y: 0.000000
rate R <-> V: 5.580728
rate N <-> D: 0.000000
rate N <-> C: 0.147632
rate N <-> Q: 4.499575
rate N <-> E: 0.000000
rate N <-> G: 0.000000
rate N <-> H: 11.201983
rate N <-> I: 1.449540
rate N <-> L: 0.000000
rate N <-> K: 5.643816
rate N <-> M: 0.000000
rate N <-> F: 0.000000
rate N <-> P: 0.000000
rate N <-> S: 26.036668
rate N <-> T: 8.951367
rate N <-> W: 0.000000
rate N <-> Y: 2.300222
rate N <-> V: 1.980479
rate D <-> C: 0.000000
rate D <-> Q: 0.000000
rate D <-> E: 46.130263
rate D <-> G: 0.000000
rate D <-> H: 64.317754
rate D <-> I: 0.000000
rate D <-> L: 0.000000
rate D <-> K: 0.000000
rate D <-> M: 0.000000
rate D <-> F: 0.000000
rate D <-> P: 0.000000
rate D <-> S: 0.000000
rate D <-> T: 0.000000
rate D <-> W: 0.000000
rate D <-> Y: 0.000000
rate D <-> V: 0.000000
rate C <-> Q: 0.000000
rate C <-> E: 0.000000
rate C <-> G: 0.000000
rate C <-> H: 0.000000
rate C <-> I: 0.000000
rate C <-> L: 0.228963
rate C <-> K: 0.000000
rate C <-> M: 0.000000
rate C <-> F: 0.000000
rate C <-> P: 0.000000
rate C <-> S: 7.609184
rate C <-> T: 0.000000
rate C <-> W: 0.000000
rate C <-> Y: 0.000000
rate C <-> V: 0.000000
rate Q <-> E: 0.000000
rate Q <-> G: 0.000000
rate Q <-> H: 0.000000
rate Q <-> I: 0.000000
rate Q <-> L: 0.000000
rate Q <-> K: 6.750657
rate Q <-> M: 0.000000
rate Q <-> F: 0.000000
rate Q <-> P: 0.000000
rate Q <-> S: 1.441509
rate Q <-> T: 0.000000
rate Q <-> W: 0.000000
rate Q <-> Y: 0.000000
rate Q <-> V: 0.000000
rate E <-> G: 38.644496
rate E <-> H: 0.000000
rate E <-> I: 0.000000
rate E <-> L: 0.000000
rate E <-> K: 1.179241
rate E <-> M: 0.000000
rate E <-> F: 0.000000
rate E <-> P: 0.000000
rate E <-> S: 0.400106
rate E <-> T: 0.000000
rate E <-> W: 0.000000
rate E <-> Y: 0.000000
rate E <-> V: 0.000000
rate G <-> H: 0.000000
rate G <-> I: 19.508616
rate G <-> L: 0.000000
rate G <-> K: 0.000000
rate G <-> M: 0.000000
rate G <-> F: 0.000000
rate G <-> P: 0.000000
rate G <-> S: 50.773946
rate G <-> T: 0.000000
rate G <-> W: 34.428614
rate G <-> Y: 0.000000
rate G <-> V: 0.000000
rate H <-> I: 0.000000
rate H <-> L: 0.097316
rate H <-> K: 0.000000
rate H <-> M: 0.000000
rate H <-> F: 5.445774
rate H <-> P: 0.000000
rate H <-> S: 0.000000
rate H <-> T: 7.315857
rate H <-> W: 0.000000
rate H <-> Y: 29.647619
rate H <-> V: 0.000000
rate I <-> L: 10.810436
rate I <-> K: 3.904031
rate I <-> M: 0.000000
rate I <-> F: 5.999061
rate I <-> P: 0.000000
rate I <-> S: 2.704311
rate I <-> T: 7.329598
rate I <-> W: 0.000000
rate I <-> Y: 1.727989
rate I <-> V: 76.785050
rate L <-> K: 0.297510
rate L <-> M: 28.315975
rate L <-> F: 4.830297
rate L <-> P: 1.066168
rate L <-> S: 2.169173
rate L <-> T: 1.133447
rate L <-> W: 4.148741
rate L <-> Y: 0.763243
rate L <-> V: 5.225005
rate K <-> M: 0.000000
rate K <-> F: 0.424109
rate K <-> P: 1.492108
rate K <-> S: 0.000000
rate K <-> T: 1.435493
rate K <-> W: 0.000000
rate K <-> Y: 1.277965
rate K <-> V: 0.000000
rate M <-> F: 0.000000
rate M <-> P: 25.560862
rate M <-> S: 0.000000
rate M <-> T: 0.000000
rate M <-> W: 0.000000
rate M <-> Y: 0.000000
rate M <-> V: 63.959439
rate F <-> P: 0.000000
rate F <-> S: 0.545275
rate F <-> T: 0.967714
rate F <-> W: 0.000000
rate F <-> Y: 2.895314
rate F <-> V: 4.977920
rate P <-> S: 14.358517
rate P <-> T: 0.000000
rate P <-> W: 0.000000
rate P <-> Y: 2.320141
rate P <-> V: 0.000000
rate S <-> T: 20.777056
rate S <-> W: 0.000000
rate S <-> Y: 0.000000
rate S <-> V: 0.000000
rate T <-> W: 4.114696
rate T <-> Y: 0.000000
rate T <-> V: 12.794694
rate W <-> Y: 0.000000
rate W <-> V: 0.000000
rate Y <-> V: 1.000000

freq pi(A): 0.052805
freq pi(R): 0.050605
freq pi(N): 0.045105
freq pi(D): 0.007702
freq pi(C): 0.017603
freq pi(Q): 0.026403
freq pi(E): 0.032124
freq pi(G): 0.006822
freq pi(H): 0.012763
freq pi(I): 0.061826
freq pi(L): 0.165232
freq pi(K): 0.087347
freq pi(M): 0.010342
freq pi(F): 0.143231
freq pi(P): 0.039384
freq pi(S): 0.074367
freq pi(T): 0.045765
freq pi(W): 0.023543
freq pi(Y): 0.046865
freq pi(V): 0.050165


ML search took 102.720271 secs or 0.028533 hours

Combined Bootstrap and ML search took 178.340924 secs or 0.049539 hours

Drawing Bootstrap Support Values on best-scoring ML tree ...



Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea



Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea

Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea
All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea

Best-scoring ML tree written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea

Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea

Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitionsBranchLabels.RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea

Overall execution time for full ML analysis: 178.355061 secs or 0.049543 hours or 0.002064 days