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.