In related news, Bill Pearson's latest release of the FASTA suite
includes support for BLAST+ like tabular output files. I guess
wrappers for these in Galaxy would also be nice to have.
---------- Forwarded message ----------
From: William Pearson <wrp(a)virginia.edu>
Date: Fri, Oct 1, 2010 at 6:26 PM
Subject: fasta-36.2.7 available
The latest version of the FASTA36 package, fasta-36.2.7, is available from:
A Mac OSX universal binary is also available.
This version of FASTA36 fixes a bug in the fastx36(_t) sub-alignment
code, that could cause the library sequence to be modified. In
addition, it fixes some problems with sub-alignments that occurred
with very short query sequences. There have also been some minor
output format changes to reduce presentation of redundant information
when multiple sub-alignments are shown. The "-L" long library
descriptions has been re-enabled, and changing the -E threshold no
longer disables multiple sub-alignments.
The major new feature in this version are the introduction of two
BLAST+ compatible tabular output formats: -m 8 (BLAST+ tabular output,
equivalent to BLAST+ -outfmt=6) and -m 8C (BLAST+ -outfmt=7).
In addition, the FASTA36 programs can be compiled to read the sequence
database only once, and then compare multiple query sequences to the
library held in memory (see comments in doc/readme.v36 and
make/Makefile36m.common). Holding the library in memory allows the
program to scale very efficiently on large multi-core computers (>40X
speedup on 48 cores).
This version of the program has not been thoroughly tested under MPI.
As always, let me know about problems.