[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

ports/94741: [ maintainer update ] update biology/fasta3

>Number:         94741
>Category:       ports
>Synopsis:       [ maintainer update ] update biology/fasta3
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Mon Mar 20 17:00:38 GMT 2006
>Originator:     Fernan Aguero
>Release:        FreeBSD 6.0-RELEASE-p4 i386

System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan_(_at_)_omega_(_dot_)_iib_(_dot_)_unsam_(_dot_)_edu_(_dot_)_ar:/usr/obj/usr/src/sys/OMEGA i386


A new version of the fasta distribution, fasta34t25d5.shar.Z, is
available from:


In general, the major changes in this version are internal; the
functions producing alignments and alignment coordinates have been
simplified.  One of the consequences is that for the parallel
versions, alignments are calculated only once, even if the alignment
information is needed several times (e.g. in the list of best scores
and as final alignments).

The major new feature is the ability to work with asymmetric scoring matrices.
Although the FASTA programs use the NxN scoring matrix format used by BLAST,
only half of the matrix was actually read  andthe rest inferred by symmetry.
This has been changed, and asymmetric matrices can be used.

In addition, the -V "*#" annotation option is now available in the
parallel versions of the programs, and some minor bug fixes are

Bill Pearson


--- fasta3.diff begins here ---
diff -u /usr/ports/biology/fasta3/Makefile fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile	Wed Mar  1 20:11:41 2006
+++ fasta3/Makefile	Mon Mar 20 13:38:06 2006
@@ -7,7 +7,7 @@
 PORTNAME=	fasta3
-PORTVERSION=	34.t25.d4
+PORTVERSION=	34.t25.d5
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.virginia.edu/pub/fasta/
diff -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo	Wed Mar  1 20:11:41 2006
+++ fasta3/distinfo	Mon Mar 20 13:38:09 2006
@@ -1,3 +1,3 @@
-MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
-SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
-SIZE (fasta34t25d4.shar.Z) = 799416
+MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7
+SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482
+SIZE (fasta34t25d5.shar.Z) = 795675
Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files
--- fasta3.diff ends here ---

freebsd-ports-bugs_(_at_)_freebsd_(_dot_)_org mailing list
To unsubscribe, send any mail to "freebsd-ports-bugs-unsubscribe_(_at_)_freebsd_(_dot_)_org"

Visit your host, monkey.org