Citing BIRCH software

Imagine if you had invented a technique and published a paper describing it, and lots of people used it without citing it. The development and refinement of computer software requires as much work as development of a lab technique, and has just as much impact on the research community. Not citing the programs you use underestimates the impact of these these programs in their fields of research. Particularly when molecular biology programs are distributed free, the only return the author gets on their time investment is your literature citation. If you use 20 different programs your work, that's like using 20 different techniques, and each one of those authors deserves a citation.

Even free software comes with a price. Citations in the literature help authors of free software:

keep their jobs
get grant money and institutional support necessary to develop new software and support existing software
attract good students, postdocs and research associates
help funding agencies make a case for supporting bioinformatics

'Nuff said. Here are some of the papers to cite for programs in BIRCH. If you can't find a citation here, look in the documentation for that program. Some programs are not written up in papers, but one should still give credit to the author.

BIRCH

BIRCH: A user-oriented, locally-customizable, bioinformatics system
Brian Fristensky
BMC Bioinformatics 2007, 8:54 (9 February 2007)
[Abstract] [PDF]

GDE

Smith, S.W., Overbeek, R., Woese, C.R., Gilbert, W., and Gillevet, P.M. (1994) The genetic data environment: an expandable GUI for multiple sequence analysis. Computer Appl. in the Biosciences 10:671-675.

FSAP Package (NUMSEQ, BACHREST, INTREST, DIGEST, TESTCODE)

Fristensky, B., Lis, J.T. and Wu, R. (1982) Portable microcomputer software for nucleotide sequence analysis. Nucl. Acids Res. 10:6451-6463.

P1HOM, P2HOM, D3HOM & D4HOM

Fristensky, B. (1986) Improving the efficiency of dot-matrix similarity searches through use of an oligomer table. Nucl. Acids Res. 14,597-610.

FASTA programs (FASTA, TFASTA, ALIGN, LFASTA, GREASE, MRTRANS, GARNIER)

Pearson, W.R. (1990) Rapid and Sensitive Sequence Comparison with FASTP and FASTA. Methods in Enzymology 183:63-98.

ClustalW , ClustalX

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680.

GenBank Database

Bilofsky, H.S. and Burks, C. (1988) The GenBank genetic sequence data bank. Nucl. Acids Res. 16:1861-1864.

MBCRR programs

See documentation files for individual programs.

Phylip

Felsenstein, J. (1989) PHYLIP Phylogeny Inference Package. Cladistics 5:164-166.

PIR/NBRF Database

Sidman, K.E. George, D.G. Barker, W.C. and Hunt, L.T. (1988) The protein identification resource (PIR). Nucl. Acids Res. 16:1869-1871.

others

See documentation file for the program.

XYLEM (FETCH, FINDKEY, FEATURES, REFORM, SPLITDB, RIBOSOME)

Fristensky, B. (1993) Feature expressions: creating and manipulating sequence datasets. Nucl. Acids Res. 21:5997-6003.