• Sequence Data
  "These sequence data were produced by the xxx Sequencing Group at the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/yyy" - where "xxx" is the name of the relevant sequencing project, such as "Human Chromosome 22" or "P. falciparum", and "yyy" is the appropriate ftp directory from which the data has been obtained. An http URL may be given in place of the ftp directory if that was the source of the data.

• Human mapping data
  "These mapping data were produced by the Chromosome * Mapping Group at the Sanger Institute and were obtained from the World Wide Web at http://www.sanger.ac.uk/HGP/Chr*." - where * is the appropriate chromosome.

If a map figure is reproduced in a publication, the figure legend should include an explicit statement concerning the source of the information.
Mapping data should be regarded as preliminary and so subject to regular update and change. It is recommended, therefore, that users carry out appropriate confirmatory checks.
If you have any questions regarding the mapping data or their use in publications, please contact the appropriate chromosome mapping group leader (details given at http://www.sanger.ac.uk/HGP/).

• "BLAST 2.04 of the NCBI Toolkit", Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and D.J. Lipman.
• "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs", Nucleic Acids Res. 25:3389-3402 (1997)

• Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) "CLUSTAL V: Improved Software for Multiple Sequence Alignment", Computer Applications in the Biosciences (CABIOS), 8(2):189-191
• Thompson J.D., Higgins D.G. and Gibson T.J. "CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice", Nucleic Acids Res. 22:4673-4680 (1994)

• B. Morgenstern, A. Dress and T. Werner (1996) "Multiple DNA and Protein Sequence Alignment Based on Segment-to-segment Comparison", Proc. Natl. Acad. Sci. USA 93, pp. 12098 - 12103
• B. Morgenstern, K. Frech, A. Dress and T. Werner (1998) "DIALIGN: Finding Local Similarities by Multiple Sequence Alignment", Bioinformatics 14, 290-294
• B. Morgenstern (1999) "DIALIGN 2: Improvement of the Segment-to-segment Approach to Multiple Sequence Alignment", Bioinformatics 15, 211 - 218.

• W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
• Pearson, W. R. (1999) "Flexible Sequence Similarity Searching with the FASTA3 Program Package" Methods in Molecular Biology

• MAC
  Gilbert, D.G. (1992) "loopDloop: A Macintosh Program for Visualizing RNA Secondary Structure -
  ftp://iubio.bio.indiana.edu/molbio/loopdloop/"
• JAVA
  Gilbert, D.G. (1996) "loopDloop in Java: A Java Application for Visualizing RNA Secondary Structure -
  ftp://iubio.bio.indiana.edu/molbio/loopdloop/java/"

• D. Lipman, S. Altschul and J. Kececioglu "A Tool for Multiple Sequence Alignment" Proc. Natl. Acad. Sci. USA 86 (1989) 4412-4415
• S. K. Gupta, J. Kececioglu, and A. A. Schaffer, "Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment" Journal of Computational Biology (1995) Vol. 2, No. 3, Pg. 459

• Zuker, M. (1989) Science 244, 48-52
• M. Zuker, D.H. Mathews and D.H. Turner "Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide" RNA Biochemistry and Biotechnology, J. Barciszewski & B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers (1999)

• Felsenstein, J. (1993) "PHYLIP (Phylogeny Inference Package) Version 3.5c" Distributed by the author. Department of Genetics, University of Washington, Seattle
  or if the editor for whom you are writing insists that the citation must be to a printed publication:
  
• Felsenstein, J. (1989) "PHYLIP - Phylogeny Inference Package (Version 3.2)" Cladistics 5: 164-166

• Brent Ewing, LaDeana Hillier, Michael C. Wendl and Phil Green. "Base-calling of Automated Sequencer Traces using Phred, 1. Accuracy Assessment" (1998) Genome Research 8:175-185
• Brent Ewing and Phil Green "Base-calling of Automated Sequencer Traces using Phred, 2. Error Probabilities" (1998) Genome Research 8:186-194

• Smith, Randall F. and Smith, Temple F. (1990) "Automatic Generation of Primary Sequence Patterns from Sets of Related Protein Sequences" PNAS 87:118-122
• Smith, Randall F. and Temple F. Smith (1992) "Pattern- Induced Multi-sequence Alignment (PIMA) Algorithm Employing Secondary Structure-dependent Gap Penalties for Comparitive Protein Modelling" Protein Engineering 5:35-41

• I.Jonassen, J.F.Collins and D.G.Higgins. "Finding Flexible Patterns in Unaligned Protein Sequences" Protein Science 4, 1587-1595 (1995)
• I. Jonassen "Efficient Discovery of Conserved Patterns Using a Pattern Graph" CABIOS 13, 509-522 (1997)

(Code available at http://www-genome.wi.mit.edu/genome_software/other/primer3.html)