Project name:
Merge reference alignments
Build separate phylogeny for each reference alignment

Advanced options

Read length Min per base coverage
Seed length Min PHRED quality
Polymorphism threshold Gap threshold

Bowtie2 parameters
(Bowtie2 documentation)
PhyML parameters
PhyML documentation)

reference genomes genome fragments/sequence reads

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.


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