Updates to MacGDE

Fixed the window size setting so MacGDE does not open larger than the viewing screen. 

Added "GDE Full or Basic menus" under the File menu so users could have GDE without all of 
the additions I have made. This removes the Phylogeny menus and lots of other programs that
I have added. You can switch between the two menu but you must open a new GDE window to see
the changes.

Modified the Import Foreign Format command so that only the data from the file is brought in 
leaving the original file alone. 
A copy of the file ending with .gde is no longer made. A WARNING is now given to remember to 
name the file with the Save As... command after importing.

Import Foreign Format now recognizes Clustal format files by using clustalw (must be present) 
included with MacGDE.

Added a View Chromat Sequence command to view chromatograms in LifeTrace. This uses a panel just 
like the Open and Import commands to locate the file and open it.

Import Chromat and View Chromat Sequence commands now handle spaces in directory (folder) names. 
But the names of the chromat files can NOT have any spaces.

DeSoete tree files now end in .tre so Treeview X will open them directly.

Changed the Mr. Bayes MCMC settings for the consensus type to be "All Compatible". 
This now matches the default settings of Mr. Bayes and often adds resolution and support to nodes.

Under PAUP the MultiCPU has been changed to 2 or 4 CPUs. Since most computers now have 2 or 4 CPUs 
I changed the run options so that the bootstraps can be run automatically. I have removed the manual 
option. Hopefully, this will make it easier for everyone to get their PAUP bootstraps done more quickly.

Added an Overwrite Database feature to the Manage DNA BLAST DataBases LOCAL and Manage Protein BLAST 
DataBases LOCAL under the Sequence Management menu. This will let you replace an entire existing database. 
Useful if you accidentally added something to a database you did not mean to. 
This has the same effect as Deleting then recreating a database, but just in one step.

Addition of New Program

Parallel Mr. Bayes (Phylogeny 1 > MrBayes3.1.2 Run Options) you can choose one processor (this runs 
regular Mr. Bayes) or 2 or 4 processors (runs pMrBayes). You will need to be running Mac OS 10.5 or better 
for this to work and have 2 or 4 processors.

PhyML 3.0 under Phylogeny 2 uses the Phylip-like interface.

ProtTest 2.1 under Phylogeny 1

SNAP: Synonymous Non-synonymous Analysis Program under the DNA/RNA menu. This program calculates 
synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences. 

Synonymous or Non-synonymous Distance Tree (SNAP) under the Phylogeny 2 menu. This uses SNAP to generate 
a ds or dn distance matrix that can be analyzed with the Neighbor program from the Phylip package to 
create trees.

Updates to Other programs

BLAST is now at version 2.2.20

CAP2 (Sequence Management>Assemble Contigs) will now maintain the name of the sequences up to 50 characters. 
!!!!!Let me know if longer names are needed!!!!

Phylip is now at version 3.68