Netview: Application Software for constructing andvisually exploring phylogenetic networks
Kirill Kryukov

kkryukov@lab.nig.ac.jp

Naruya Saitou

nsaitou@genes.nig.ac.jp

Division of Population Genetics, National Institute of Genetics/ Department of Genetics, Graduate University for
Advanced Studies, Mishima, 411-8540 Japan

Keywords: phylogenetic network, neighbor-joining method

1Introduction

Reconstructing evolutionary history of a group of species is a major task in biological study. Many methods
exist for reconstructing such history, or phylogeny, but most of them are based on an assumption thatevolution of given gene family can be represented as a tree. However some families of genes may havealternative historical structure that cannot be represented as a tree. Such history can result from events suchas recombination, gene conversion and horizontal gene transfer, and require not tree but network for accurate
representation. Parallel substitutions are also sources of non-tree networks. For the purpose of understanding
such history we developed a program Netview, which enables constructing phylogenetic network based on
the sequence data.

2Netview

Netview uses following approach to construct a network: First, it constructs a NJ-tree [1] for provided set ofsequences, using nucleotide difference distance matrix (Fig. 1). Then every nucleotide site position ofsequence data is analyzed to check if it is compatible with the NJ-tree constructed. Sites that show
incompatible partitioning configuration, are then listed for user’s selection. When the site is selected by user,
the initial NJ-tree is morphed into a network by splitting its nodes into two planes (Fig. 2). Two planes
correspond to the sequence partitioning pattern, obtained from the given nucleotide site position. Tree nodes
are assigned to the planes, according to the partitioning pattern of selected nucleotide site. Structure
constructed in this way is no longer tree, but network, which is positioned in a 3D space. Netview program
then enables user to view the network from different angles.
Netview has following features to support constructing and exploring phylogenetic networks:
1. Rotating network around any of 3 axes.
2. Shifting network structure to the left, right, upward or downward.
3. Zooming in and out
4. Take screenshot of current view.
5. Changing to another partitioning pattern, taken from different nucleotide position. The network isreconstructed based on the same initial tree.

Figure 1: Initial NJ-tree used as a basis to build the network. On the right hand there is a table of partitioning
patterns (designated with binary characters) that are present in the sequence data. Partitions 1-5, 7, and 8
are compatible with the NJ tree, while partitions 6, 9, 10 are not. (Example sequences are from [2])Figure 2. Example phylogenetic network, produced with Netview.

Partition no. 6 was chosen.

Netview is written in C and has it’s source will be open. Currently only a windows version exists, but it iswritten in a way making it easy to port the program to other OS, like Linux or MacOS. Netview can accept
sequence data with FASTA-format or ClustalW multiple alignment format. The latest version of Netview isavailable from the program web-site [3].

References[1] Saitou, N. and Nei, M., The neighbor-joining method: A new method for reconstructing phylogenetictrees, Molecular Biology and Evolution, 4:406-425, 1987
[2] Saitou, N. and Yamamoto, F.-I., Evolution of primate ABO blood group genes and their homologous
genes, Molecular Biology and Evolution, Vol. 14, No. 4, pp. 399-411, 1997
[3] http://esper.lab.nig.ac.jp/netview/