Just FYI, 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. Peter ---------- Forwarded message ---------- From: William Pearson <wrp@virginia.edu> Date: Fri, Oct 1, 2010 at 6:26 PM Subject: fasta-36.2.7 available To: fasta_list@virginia.edu The latest version of the FASTA36 package, fasta-36.2.7, is available from: http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.2.7.tar.gz 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. Bill Pearson