4 New programs - tfastx3, tfastx3_t, compare a protein sequence to
5 forward and reverse translations of a DNA sequence database. An excellent
6 replacement for tfasta3.
8 Sun multiprocessing - change in thr_create() to use all CPU's if available.
10 GCG formats - now can search with simple GCG-format query sequences and
11 results with GCG format Swissprot and Genpept are more readable.
15 Fixed bugs in tfastx3(_t) and fastx3(_t) including an ancient problem
16 with aatran(). Less redundancy in gcg_ranlib().
21 Included support for BLOSUM62 (-s BL62) as per documentation.
23 Rearranged Makefile's so that they would make everything in one pass.
27 Corrected yet another problem with the fastx/tfastx code.
29 Noticed that searching without optimized scores gave no optimized
30 scores on the final list of scores - fixed this.
32 The pvm version now does alignments - not thoroughly tested.
36 Fixed display of best scores to stdout.
38 Fixed problem with alignments when -o flag used.
40 pvcompfa/pvcompsw have now been tested on DEC Alpha, Solaris X86, and
41 SGI PVM implementations. Several bugs were corrected.
45 Fixed bug selectbestz() that caused core dumps in pvcomplib.c
46 (changes to pvcomplib.c, comp_thr.c, complib.c).
50 Corrected showalign.c/pvm_showalign.c addressing bug found and fixed
51 by Erik Wallin. (erikw@biokemi.su.se).
55 Corrected bug so alternative scoring matrices are used.
59 Remove singularities from regression routine.
61 -z 0 now means no statistics (same as -z -1).
63 No longer show alignment for 0 score.
67 Fix problem with -b, -d when Z-values disabled.
71 Altschul-Gish statistical estimates (-z 3) now work properly.
73 Fix problem with mean_var==0.0.