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Bowtie2 documentation
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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.

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

Terms of use

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:

  1. The REALPHY webserver will be used by you and/or your institution solely for non-commercial purposes, except with express permission from the authors.
  2. You may provide us with feedback on the use of the REALPHY webserver in your research, and we are permitted to use any information you provide in making changes to REALPHY.
  3. Any risk associated with using the REALPHY webserver is with you and your institution.
  4. Any results produced with REALPHY are licenced under CC BY-NC 4.0 .
  5. The REALPHY webserver should be cited in any publication(s) reporting on data obtained by using it as:

    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.

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