Bug 94741 - [ maintainer update ] update biology/fasta3
Summary: [ maintainer update ] update biology/fasta3
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: freebsd-ports-bugs (Nobody)
Depends on:
Reported: 2006-03-20 17:00 UTC by Fernan Aguero
Modified: 2006-03-20 22:23 UTC (History)
0 users

See Also:

fasta3.diff (1010 bytes, patch)
2006-03-20 17:00 UTC, Fernan Aguero
no flags Details | Diff

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Description Fernan Aguero 2006-03-20 17:00:38 UTC

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
Comment 1 Pav Lucistnik freebsd_committer 2006-03-20 22:23:32 UTC
State Changed
From-To: open->closed

Committed, thanks!