PhageGE Phage Genome Exploration
This repository contains all example data which was used in the demonstration of functions from PhageGE.
All the example datasets are under the Example data folder or you can download the compressed example dataset in Example data.zip.
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Phage phylogeny estimation The input files will be all phage WGS data which you want to use for the phylogeny estimation. The WGS data should be in the .fna or .fasta format. a.Click the Browse to select all phage WGS data you would like to include. b.You will be able to explore the tree by clicking 'Explore Tree' after completing WGS data upload
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Phylogenetic tree visualisation The input files include a tree file “.tre” obtained from phylogenetic analysis (whether generated by PhageGE or other phylogenetic analysis pipeline) and a sample information file named “sample_info.csv” containing the taxonomy information. a.Click the Browse to select the tree file as well as its related sample/sequence information file you would like to visualise. b.You will be able to interactively visualise your data by clicking 'Explore Tree' after completing data upload.
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Lifestyle prediction The input file will be phage WGS data (in ".fasta or .fna" ) you would like to explore its lifestyle. a.Click the Browse to select phage WGS data which you want to predict lifestyle. b.You will be able to get the lifestyle prediction result by clicking 'Explore Lifestyle prediction' after completing data upload.
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Annotation comparison The input file will be phage phage genome annotation files obtained from different pipelines. a.Click the Browse to select phage genome annotation files which you want to perform the comparison. b.You can select either "Unique" or "Common" options to identify the common and different annotations from different phage genome annotation pipelines.
