Supporting data and code for: Phylogenetic identification of influenza virus candidates for seasonal vaccines

This repository contains the code, data and materials developed for 'Phylogenetic identification of influenza virus candidates for seasonal vaccines'. We downloaded all hemagglutinin (HA) and neuraminidase (NA) human H3N2 sequences collected from 1980 to February 2020 from the Global Initiative on Sharing Avian Influenza Data (GISAID). Accession numbers and references to the GISAID submitting laboratories for the sequences used in this study are included in this repository. As per GISAID access terms, the sequences used in this study are not reproduced here but may be downloaded from the GISAID server.This repository contains all code to compute the features, train and test the machine learning models, predict the next year's flu vaccine candidates, and generate the plots for the paper. Derived data e.g. all the influenza trees for the experiments in years 2016 to 2020 are included.

本仓库包含为《季节性疫苗候选流感病毒的系统发育鉴定》所开发的代码、数据与相关材料。我们从全球共享所有流感数据倡议（Global Initiative on Sharing Avian Influenza Data, GISAID）下载了1980年至2020年2月期间收录的全部人类H3N2亚型流感病毒的血凝素（hemagglutinin, HA）和神经氨酸酶（neuraminidase, NA）序列。本仓库收录了本研究使用序列的登录号以及GISAID提交实验室的相关引用信息。根据GISAID的使用条款，本研究使用的序列未在此仓库中直接复现，可从GISAID服务器下载。本仓库包含所有用于计算特征、训练与测试机器学习模型、预测下一季流感疫苗候选株以及生成论文所需图表的代码。此外还包含衍生数据，例如2016年至2020年各实验所用的全部流感系统发育树。