Figure. Molecular Phylogenetic analysis of the hsp65 sequences from 181 species/subspecies of Mycobacteriumby with Maximum Likelihood method
The evolutionary history was inferred by using the Maximum Likelihood method based on the Jukes-Cantor model [1]. The tree with the highest log likelihood (-10804.80) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 182 nucleotide sequences rooted with Nocardia farcinica IFM 10152(T). Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 400 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [2].
1. Jukes T.H. and Cantor C.R. (1969). Evolution of protein molecules. In Munro HN, editor, Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
2. Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution (https://doi.org/10.1093/molbev/msy096).
Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided "as is" without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.
The evolutionary history was inferred by using the Maximum Likelihood method based on the Jukes-Cantor model [1]. The tree with the highest log likelihood (-10804.80) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 182 nucleotide sequences rooted with Nocardia farcinica IFM 10152(T). Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 400 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [2].
1. Jukes T.H. and Cantor C.R. (1969). Evolution of protein molecules. In Munro HN, editor, Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
2. Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution (https://doi.org/10.1093/molbev/msy096).
Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided "as is" without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.
The fasta file below contains maunually currated hsp65 sequences from 185 species/subspecies of Mycobacterium.
May 6, 2018
hsp65_185.fas | |
File Size: | 80 kb |
File Type: | fas |