Phylogenetic Tree

1 Introduction

Phylogenetic Tree takes aligned antibody sequences as input to construct a phylogenetic tree diagram, which aids in analyzing the evolutionary relationships between the sequences and reveals the origins and evolutionary processes of the antibodies. The phylogenetic inference methods include NJ (Neighbor Joining), UPGMA (Unweighted Pair Group Method with Arithmetic Mean), ME (Minimum Evolution), ML (Maximum Likelihood), and MP (Maximum Parsimony).

2 Parameters

• Sequences：Input aligned sequences. If misalignments are detected, it will default to using Multiple Sequence Alignment module for alignment first.
• Statistical Method：
  • NJ¹: The Neighbor Joining method is a distance-based approach for reconstructing phylogenetic trees from evolutionary distance data. The core idea is to find, at each stage of clustering, the pair of operational taxonomic units (OTUs) that minimize the total branch length, known as "neighbors," and merge them. NJ is favored for its fast computation speed and relatively high accuracy, especially when dealing with smaller evolutionary distances and shorter sequences. It may be sensitive to outliers but remains popular.
  • UPGMA²: Unweighted Pair Group Method with Arithmetic Mean is a hierarchical clustering method for evaluating phylogenetic relationships. The core idea is to gradually build a clustering tree by calculating the average distance between samples.
  • ME³: Minimum Evolution is a distance-based method for constructing phylogenetic trees. The core idea is to find a phylogenetic tree that minimizes the total length of all branches, aiming to find the most likely evolutionary path by minimizing the total evolutionary distance.
  • ML⁴: Maximum Likelihood uses dynamic programming algorithms to efficiently compute likelihood values, inferring phylogenetic trees by maximizing the likelihood function of the sequences, providing a statistically rigorous method for tree construction.
  • MP⁵: Maximum Parsimony, based on Occam's Razor principle, seeks the tree that requires the fewest evolutionary steps to explain the observed variations. The author believes that the most parsimonious tree is the one most likely to reflect the true evolutionary history.

3 Results Explanation

• Chart: Phylogenetic Tree Chart.
• Newick.nwk: Newick format tree file.

Figure 1. Result of Phylogenetic Tree example.

4 Reference

[1] Saitou, N., & Nei, M. (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4(4), 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
[2] Sokal, R. R., & Michener, C. D. (1958). A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38(1), 1409-1438.
[3] Rzhetsky, A., & Nei, M. (1992). A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution, 9(5), 945-967. https://doi.org/10.1093/oxfordjournals.molbev.a040771
[4] Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376. https://doi.org/10.1007/bf01734359
[5] Fitch, W. M., & Margoliash, E. (1967). Construction of phylogenetic trees. Science, 155(3761), 279-284. https://doi.org/10.1126/science.155.3760.279