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About Algorithms for Molecular Biology

This page includes information about the aims and scope of Algorithms for Molecular Biology, editorial policies, open access and article-processing charges, the peer review process and other information. For details of how to prepare and submit a manuscript through the online submission system, please see the instructions for authors.

Aims & scope

Algorithms for Molecular Biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning.

Areas of interest include but are not limited to: algorithms for RNA and protein structure analysis, gene prediction and genome analysis, comparative sequence analysis and alignment, phylogeny, gene expression, machine learning, and combinatorial algorithms.

Where appropriate, manuscripts should describe applications to real-world data. However, pure algorithm papers are also welcome if future applications to biological data are to be expected, or if they address complexity or approximation issues of novel computational problems in molecular biology. Articles about novel software tools will be considered for publication if they contain some algorithmically interesting aspects.

Open access

All articles published by Algorithms for Molecular Biology are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. Further information about open access can be found here.

Authors of articles published in Algorithms for Molecular Biology are the copyright holders of their articles and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate the article, according to the BioMed Central copyright and license agreement.

For authors who are US government employees or are prevented from being copyright holders for similar reasons, BioMed Central can accommodate non-standard copyright lines. Please contact us if further information is needed.

Article-processing charges

The publication costs for Algorithms for Molecular Biology are covered by the journal, so authors do not need to pay an article-processing charge.

Indexing services

All articles published in Algorithms for Molecular Biology are included in PubMed, the most widely used biomedical bibliographic database service, which is run by the US National Library of Medicine. Other bibliographic databases that index articles published in Algorithms for Molecular Biology include:

  • ACM
  • Biological Abstracts
  • CAS
  • Citebase
  • DBLP
  • DOAJ
  • Google Scholar
  • OAIster
  • PubMed
  • PubMed Central
  • Science Citation Index Expanded
  • SCImago
  • Scopus
  • Zetoc

The full text of all research articles is deposited in PubMed Central, the US National Library of Medicine's full-text repository of life science literature, and other digital archives including e-Depot (The Netherlands).

The full text of all research articles published by BioMed Central is also available on SpringerLink.

Algorithms for Molecular Biology is tracked by Thomson Reuters (ISI) and has an Impact Factor of 1.44.

Publication and peer review process

Content overview

Algorithms for Molecular Biologyconsiders the following types of articles:<ul

  • Research: these articles should present original research work on the development and analysis of novel algorithms in bioinformatics. In general, the usefulness of algorithms should be demonstrated by applications to biological data. However, purely theoretical manuscripts are also welcome if future applications to problems in molecular biology are to be expected or if they address complexity or approximation issues of novel computational problems in molecular biology. Clear writing and understandable algorithm description are of particular importance. Unclearly written manuscripts and manuscripts with substantial grammatical errors will be immediately rejected, regardless of their possible scientific content. Although authors are asked to prepare manuscripts according to our Instructions for authors, we do allow some flexibility. In particular, our journal has no standardised section headings. Authors are free to use the manuscript structure and section headings that they think are appropriate for their article.
  • Review articles: these articles should give a general overview on a sub-field of algorithmic bioinformatics. In general, reviews are invited by the Editorial Board, but proposals for review articles are welcome.
  • Editorials: short articles written by the Editor(s)-in-Chief and selected members of the Editorial Board. These articles highlight new developments in the journal.
  • Book reports: short summaries of the strengths and weaknesses of a book; they should evaluate its overall usefulness to the intended audience. As review articles, book reports are usually invited by the editors.
  • Commentaries: short, focused and opinionated articles on any subject within the journal's scope. These articles are usually related to a contemporary issue, such as recent research findings, and are often written by opinion leaders invited by the Editorial Board.
  • Debate articles: these articles present an argument that is not essentially based on practical research. Debate articles can report on all aspects of the subject including political, sociological and ethical aspects.
  • Meeting report: short reports on conferences that the authors have attended, usually invited by the Editorial Board. It is best for these articles to be published as soon after the meeting as possible, and they should focus on the key developments presented and discussed at the meeting.
  • Short reports: brief reports of data from original research, usually about 1500 words.
  • Software articles: these papers should describe newly developed software tools or substantial improvements to existing tools. They should contain some algorithmic novelty; manuscripts about web servers, graphical user interfaces etc. will not be considered.

    Peer-review policies

    The Editor-in-Chief will send submitted manuscripts to an associate editor responsible for the field, who will manage the editorial and refereeing procedure. The associate editor will send the manuscript to two or three referees and will ensure that the reports are returned within three weeks. The associate editor managing a manuscript will be responsible for the final decision about acceptance or rejection of the manuscript.

    Edited by Burkhard Morgenstern and Peter Stadler, Algorithms for Molecular Biology is supported by an expert Editorial Board.

Authors will be able to check the progress of their manuscript through the submission system at any time by logging into My Algorithms for Molecular Biology, a personalized section of the site.


High-quality, bound reprints can be purchased for all articles published. Please see our reprints website for further information about ordering reprints.


Algorithms for Molecular Biology will consider supplements based on proceedings (full articles or meeting abstracts), reviews or research. All articles submitted for publication in supplements are subject to peer review. Published supplements are fully searchable and freely accessible online and can also be produced in print. All full length articles (proceedings, reviews or research articles) are indexed by PubMed. PubMed displays the title of the supplement only in the case of meeting abstract collections. For further information, please contact us.

Editorial policies

All manuscripts submitted to Algorithms for Molecular Biology should adhere to BioMed Central's editorial policies.

Citing articles in Algorithms for Molecular Biology

Articles in Algorithms for Molecular Biology should be cited in the same way as articles in a traditional journal. Because articles are not printed, they do not have page numbers; instead, they are given a unique article number.

Article citations follow this format:

Authors: Title. Algorithms Mol Biol [year], [volume number]:[article number].

e.g. Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, Griffin JL: Increased hepatic oxidative metabolism distinguishes the action of Peroxisome Proliferator-Activated Receptor delta from Peroxisome Proliferator-Activated Receptor gamma in the Ob/Ob mouse. Algorithms Mol Biol 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Algorithms for Molecular Biology?

High visibility

Algorithms for Molecular Biology's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience. Articles that have been especially highly accessed are highlighted with a 'Highly accessed' graphic, which appears on the journal's contents pages and search results.

Speed of publication

Algorithms for Molecular Biology offers a fast publication schedule whilst maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles will be published with their final citation after acceptance, in both fully browsable web form, and as a formatted PDF; the article will then be available through Algorithms for Molecular Biology, BioMed Central and PubMed Central and will also be included in PubMed.


Online publication in Algorithms for Molecular Biology gives authors the opportunity to publish large datasets, large numbers of color illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other articles).

Promotion and press coverage

Articles published in Algorithms for Molecular Biology are included in article alerts and regular email updates. Some may be included in abstract books mailed to academics and are highlighted on Algorithms for Molecular Biology's pages and on the BioMed Central homepage.

In addition, articles published in Algorithms for Molecular Biology may be promoted by press releases to the general or scientific press. These activities increase the exposure and number of accesses for articles published in Algorithms for Molecular Biology. A list of articles recently press-released by journals published by BioMed Central is available here.

Authors of articles published in Algorithms for Molecular Biology retain the copyright of their articles and are free to reproduce and disseminate their work (for further details, see the BioMed Central copyright policy and license agreement).

For further information about the advantages of publishing in a journal from BioMed Central, please click here.