Version 0.960718 contains the following significant modifications:

1) There have been improvements in memory usage and speed that should
substantially facilitate phrap and cross_match analyses of large
datasets. Cross_match can now be used for database searches.
 These changes required a fair amount of reorganization of the
internal data structures. In the course of making them, I have had to
temporarily inactivate the phrap option that allowed one set of reads
to be assembled against a second set of sequences (e.g. reference
sequences being scanned for polymorphisms), using two or more input
files. This will be restored soon.

2) Swat has been improved in several ways. I have restored and
improved its ability to compute z-scores and E values for database
searches, and these now appear to be quite reliable.  Also, it is now
possible to use swat for profile searches (with the restriction that
gap penalties still need to be position independent).

3) A graphical viewer for phrap assemblies, "phrapview", is now
included. This is intended to complement the "local" view of the
assembly provided by consed, by giving a "global" view that focusses
on information pertaining to possible incorrectness, incompleteness,
or non-uniqueness of the assembly.  Phrapview displays depth of
coverage, forward-reverse read pairs, significant pairwise matches
involving reads in different locations, and chimeric reads. It
requires a ".view" file produced by running phrap with the -view
option.  Phrapview is written in perl-tk and to run it you will need to
have installed on your system a recent version of perl that includes
the tk library (available for free from a number of web sites).
Further documentation appears in the file "general.doc". The program
was written rather hastily (in less than a week, including the time to
learn perl and Tk) and I would appreciate any feedback on how to make
it more useful.

4) The following known bugs have been fixed:
 (i) A bug that caused occasional crashes in the "Revising contigs" phase.
 (ii) Another bug in revise_contigs that occasionally caused premature
truncation of the contig sequence, resulting in massive pileups of
reads at the truncated end; and that also caused a lower quality read
to occasionally be used in place of a higher quality one in deriving
the contig sequence.
 (iii) A bug that caused an infinite loop on data readin on SGI
machines (N.B. I don't have access to an SGI computer and so haven't
been able to verify that the programs now run successfully -- please
let me know if there are still problems).
 (iv) A bug that caused premature termination of phrap when there are
0 length reads in the dataset.
 Please continue to report any bugs to me. 

5) Contig base quality information is now output in the .ace file (as
well as the .contigs.qual file). You need to obtain a new version of
consed from David Gordon (which he is distributing this week) in order
to avoid having consed crash on these .ace files. (This version of
consed does not yet actually use the contig base quality information).

6) Phrap, cross_match and swat are now all case insensitive, in the
sense that all sequences are immediately converted to upper case on
readin. The -use_case option is no longer available. If you were
previously using that, you will need to create .qual files that
contain the information instead. In any case (so to speak!) I strongly
recommend that you use phred's quality values which are substantially
more discriminating.