Эволюционные модели и дистанции между последовательностями биополимеров

Август 8, 2022

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Эволюционные модели и дистанции между последовательностями биополимеров

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5. Для анализа с использованием метода максимального правдоподобия, параметр «branch swap filter» используется для установки строгости оптимизации
16. Gp 2 0.008 0.002 Gp 1 0.020 0.004 4a 0.039 0.008 4b 0.017 0.004 Table. Estimates
17. [1] #Gp_2 [2] #Gp_1 [3] #4a [4] #4b [ 1 2 3 4 ] [1] [
18. Таблица 1. Матрица средних значений генетических расстояний (число нуклеотидных замен на сайт) между генотипами HAstV. В
22. Figure. Evolutionary relationships of taxa The evolutionary history was inferred using the Neighbor-Joining method [1]. The
35. (((C:3.2,D:8.0):5.5,E:7.7):5.2,(A:6.1,B:6.3):7.5); длины ветвей (((C,D),E)),(A,B)); только топология Newick tree format (Скобочная формула) A B C D E
37. http://www.iqtree.org/
42. Скачать презентацию

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Для анализа с использованием метода максимального правдоподобия, параметр «branch swap filter»

используется для установки строгости оптимизации относительно длины ветви. Более слабый фильтр приведет к более исчерпывающей оптимизации, однако поиск может занять больше времени, но потенциально, большее пространство будет изучено.

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Gp 2 0.008 0.002
Gp 1 0.020 0.004
4a 0.039 0.008
4b 0.017 0.004
Table.

Estimates of Average Evolutionary Divergence over Sequence Pairs within Groups
The number of base substitutions per site from averaging over all sequence pairs within each group are shown. Standard error estimate(s) are shown in the last column. Analyses were conducted using the Maximum Composite Likelihood model [1]. The analysis involved 23 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 2306 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [2].

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[1] #Gp_2
[2] #Gp_1
[3] #4a
[4] #4b
[ 1 2 3 4 ]
[1] [

0.008 ][ 0.017 ][ 0.019 ]
[2] 0.042 [ 0.018 ][ 0.020 ]
[3] 0.091 0.099 [ 0.015 ]
[4] 0.104 0.111 0.082
Table. Estimates of Evolutionary Divergence over Sequence Pairs between Groups
The number of base substitutions per site from averaging over all sequence pairs between groups are shown. Standard error estimate(s) are shown above the diagonal. Analyses were conducted using the Maximum Composite Likelihood model [1]. The analysis involved 23 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 2306 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [2].

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Таблица 1. Матрица средних значений генетических расстояний (число нуклеотидных замен на

сайт) между генотипами HAstV. В квадратных скобках приведено стандартное отклонение, рассчитанное по 1000 реплик.
1 2 3 4 5 6 8
[1]
[2] 0.259 [ 0.008]
[3] 0.228 [ 0.007] 0.241 [ 0.007]
[4] 0.236 [ 0.007] 0.271 [ 0.007] 0.269 [ 0.009]
[5] 0.232 [ 0.006] 0.276 [ 0.008] 0.236 [ 0.008] 0.251 [ 0.007]
[6] 0.329 [ 0.010] 0.335 [ 0.009] 0.318 [ 0.010] 0.362 [ 0.010] 0.309 [ 0.010]
[8] 0.201 [ 0.007] 0.241 [ 0.008] 0.230 [ 0.009] 0.164 [ 0.005] 0.207 [ 0.006] 0.322 [ 0.009]
Таблица 2. Средние значения генетических расстояний (число нуклеотидных замен на сайт) внутри генотипов HAstV. В квадратных скобках приведено стандартное отклонение, рассчитанное по 1000 реплик.
HastV-1 0.085 [0.002]
HastV-2 0.174 [0.004]
HastV-3 0.025 [0.001]
HastV-4 0.085 [0.003]
HastV-5 0.081 [0.004]
HAstV-6 0.055 [0.002]

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Figure. Evolutionary relationships of taxa
The evolutionary history was inferred using the

Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 2.17322002 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura-Nei method [3] and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 4). The differences in the composition bias among sequences were considered in evolutionary comparisons [4]. The analysis involved 31 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 2241 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [5].

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