Phylogenetics toolbox

Web interface for running phylogenetic inference tools. Select a tool below to get started.

• GS::Graph Splitting Method v2.5

  Graph Splitting is a graph-based phylogenetic tree inference method. As input, it accepts not only nucleotide or amino acid sequences, but also distance matrices and similarity matrices.

• PANJEP::PA-based NJ with EP v1.0

  PANJEP is Pairwise Alignment-based Neighbor Joining with Edge Perturbation. First, instead of using a multiple sequence alignment (MSA), the PANJEP estimates a distance matrix based on all-to-all pairwise alignments. Next, a phylogenetic tree is inferred using the Neighbor-Joining (NJ) method, and the reliability of internal branches is evaluated using the Edge Perturbation (EP) method.

• SJ::Splitting and Joining Method v0.1

  Hybrid GS + PANJEP tree inference: each clade is resolved by graph splitting (GS) or neighbor-joining (PANJEP) according to its similarity-matrix transitivity.

Download

The standalone version is available here.

Citation

If you use Graph Splitting method in your research, please cite:
Motomu Matsui, Wataru Iwasaki (2020) Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction, Systematic Biology, 69(2):265–279

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