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Port details
ariadnePrograms to compare protein sequences and profiles
1.3biologyΣ=0 1.3Version of this port present on the latest quarterly branch.
BROKEN: No public distfiles DEPRECATED: Broken for more than 6 months This port expired on: 2018-06-06 IGNORE: is marked as broken: No public distfiles
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
ARIADNE is a package of two programs, ariadne and prospero, that compare
protein sequences and profiles using the Smith-Waterman algorithm, and
assesses statistical significance using a new accurate formula,
described in Mott, 2000, "Accurate Formula for P-values of gapped local
sequence and profile alignments" J. Mol Biol. 300:649-659.
The sequence/profile comparison algorithms used in ARIADNE are standard,
and are probably not the fastest implementations available. The novel
part is the method for determining statistical significance, which will
give thresholds of significance that are accurate to within 5% 95% of
the time.
The package is written in ANSI C. You are free to incorporate the method
used for assessing statistical significance into third-party code,
provided you cite the above reference. The routines for assessing
significance are all in gaplib.c
WWW: http://www.well.ox.ac.uk/ariadne/
===> The following configuration options are available for ariadne-1.3:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
Remove expired ports:
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring
comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above )
Cleanup $() variables in ports Makefiles.
Mostly replace with ${}, but sometime, replace with $$() because it is
what was intended in the first place. (I think.)
Sponsored by: Absolight
misc/otter & biology/ariadne: Not jobs safe
The otter port tries to build libotter.a before an object is completely
built (share.o in my case) and ariadne tries to start building in a
directory before it is created (under multiple jobs).
Add ariadne 1.3, programs to compare protein sequences and
profiles, using the Smith-Waterman algorithm.
PR: ports/67811
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
