What is new with Consed 20.0:

-Better method of fixing the consensus and read alignments at the ends
 of contigs.  Particularly useful after adding new reads. (see
 -fixContigEnds in README.txt)

-fixes problem reading MIRA assembly output.  A version of Velvet
 produces consed-ready ace files.

-Ability of autoedit to fix repeated base errors in consensus such as
 this:

 consensus: ccc
 read1:     cc*
 read2:     *cc 

-Solexa (Illumina) reads can be edited and tagged

-The consensus can be directly edited (ambiguity codes are allowed).

-Batch changing consensus:  You must supply a file of consensus
 positions to change

-allows extrememly high depth of coverage (over 32,000 reads
 deep)

-add454Reads.perl used to add all of the 454 reads in an sff file.
 Now it also allows you to specify particular reads.

-Sorting of reads.  By default reads are now sorted by a quality
  window about the cursor.  In the Aligned Reads window, there is a
  "sort" menu allowing the ability to easily switch from one kind of
  sort to another.  There is an indicator of which type of sort is
  currently used.  Reads can also be sorted by base at the cursor
  position which is useful for snp and genotype calling.

-Search for Highly Discrepant Positions now has the option of
  excluding positions in which the consensus has an x or an n (or any
  user-specified base).  This is also available via autoreport.
  Search for string removes any "*" characters before searching.

-Tears and joins: when making these, tags are added with lots of
  information in the comment (old contig name, # of reads, and # of
  base pairs, new contig name, # of reads, # of base pairs, etc)

-selectRegions.perl: Allows multiple sequences in the same fasta file.
 Consensus positions, instead of starting at 1, start at position with
 respect to original big sequence

-Main Consed Window's Contig List:  there is now a button that
  toggles the order from ordered by number of reads to ordered by
  contig name (Contig5, Contig6, Contig7,...)

-Saving highlighted read names to a file.  In the Aligned Reads Window
  under the Misc menu is this feature.    You are given a choice of just
  saving the reads in the current contig or in the entire assembly.

-Aligned Reads Window:  Click on a read base and a horizontal line
  will appear, aiding your eye in following along the read and finding
  the corresponding read name.  This can be turned off.

-Shift-click to select multiple contigs for "Remove Contigs".
 Shift-click to select multiple scaffolds in Assembly View's Reorient
 Contigs.

-bug fixes, improved error messages, and performance improvements