REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide a small number of reference genomes in either FASTA or Genbank format (contigs or fully sequenced genomes) as well as a number of other query genomes which can be in FASTQ (short reads), FASTA or Genbank format. All provided sequences (references and queries) will then be mapped to each of the references via bowtie2. From these alignments multiple sequence alignments will be reconstructed from which phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites will be available for download after the program has finished. Furthermore the user has the option to combine individual reference alignments by ticking the merge box. This will combine different reference genome alignments and hence increase the quality of the inferred phylogeny. However, this option is very time and RAM intensive.
Citation:
Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014
Escherichia coli from Touchon et al. 2009
Pseudomonas syringae from Baltrus et al. 2011
The developers of the REALPHY give permission to you and your institution to use the REALPHY webserver for internal, research purposes, on the following conditions:
Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, and Erik van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution; Published online 5 March 2014
Commercial users should contact us for licensing arrangements.
