Citing BIRCH software
Imagine if you had invented a technique and published a paper
it, and lots of people used it without citing it. The development
of computer software requires as much work as development of a lab
and has just as much impact on the research community. Not citing
you use underestimates the impact of these these programs in their
of research. Particularly when molecular biology programs are
free, the only return the author gets on their time investment is
literature citation. If you use 20 different programs your work,
like using 20 different techniques, and each one of those authors
comes with a price. Citations in the
help authors of free software:
'Nuff said. Here are some of the papers to cite for programs in
If you can't find a citation here, look in the documentation for
Some programs are not written up in papers, but one should still
to the author.
- 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
BIRCH: A user-oriented,
locally-customizable, bioinformatics system
BMC Bioinformatics 2007, 8:54 (9 February 2007)
FSAP Package (NUMSEQ, BACHREST, INTREST, DIGEST, TESTCODE)
Fristensky, B., Lis, J.T. and Wu, R. (1982) Portable microcomputer
for nucleotide sequence analysis. Nucl. Acids Res. 10:6451-6463.
P1HOM, P2HOM, D3HOM & D4HOM
Fristensky, B. (1986) Improving the efficiency of dot-matrix
searches through use of an oligomer table. Nucl. Acids Res.
FASTA programs (FASTA, TFASTA, ALIGN, LFASTA, GREASE, MRTRANS,
Pearson, W.R. (1990) Rapid and Sensitive Sequence Comparison with
and FASTA. Methods in Enzymology 183:63-98.
ClustalW , ClustalX
Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W:
the sensitivity of progressive multiple sequence alignments through
weighting, position specific gap penalties and weight matrix choice.
Acids Res. 22:4673-4680.
Bilofsky, H.S. and Burks, C. (1988) The GenBank genetic sequence
Nucl. Acids Res. 16:1861-1864.
Felsenstein, J. (1989) PHYLIP Phylogeny Inference Package.
Sidman, K.E. George, D.G. Barker, W.C. and Hunt, L.T. (1988) The
identification resource (PIR). Nucl. Acids Res. 16:1869-1871.
See documentation file for the program.
XYLEM (FETCH, FINDKEY, FEATURES, REFORM, SPLITDB, RIBOSOME)
Fristensky, B. (1993) Feature expressions: creating and manipulating
datasets. Nucl. Acids Res. 21:5997-6003.