Return to MacGDE
The Downloads page contains the complete installer for MacGDE.
Everything is now Universal.
Below is a list of programs included with this download. I hope to add more programs over time, or at least links and menus. So if you compile a program to run under MacOS X let me know and I will add it in. Programs that take input from the command line or that will read instructions from a file are easily added to MacGDE. Programs that will only accept input from their own menu system can be added but the program will most likely be limited to launching and reading a sequence alignment file only.
Program (Download) See Note 3 below |
Supplied |
Menu Present |
Source |
BLAST 2 Sequences Genbank |
NA |
Yes
DNA/RNA Protein |
|
BLAST GenBank |
NA |
Yes
DNA/RNA Protein |
|
BLAST MultiSequences GenBank |
NA |
Yes
DNA/RNA Protein |
|
BLAST 2 Sequences LOCAL Updated 09-05-14 |
NA |
Yes
DNA/RNA Protein |
|
BLAST DNA Databases LOCAL Updated
09-05-14 |
NA |
Yes
DNA/RNA |
|
BLAST Protein Databases
LOCAL Updated
09-05-14 |
NA |
Yes Protein |
|
BootScanning |
Yes |
Yes |
|
Boxshade 3.2 |
Yes |
Yes |
|
CAP2 |
Yes |
Yes |
|
ClustalW
1.83 |
Yes |
Yes DNA/RNA Protein |
|
DBSTAT (BIRCH Package) amino acid freq. |
Yes |
Yes |
|
DeSoete Tree Fit Updated 09-05-14 |
Yes |
Yes |
|
Distance Scannin |
Yes |
Yes |
|
Dot Plot Tool |
Yes |
Yes |
|
fastDNAml |
Yes |
Yes |
|
Fetch Sequence from GenBank |
NA |
Yes |
|
Find All (Enhanced) |
Yes |
Yes DNA/RNA Protein |
|
GapCoder |
Yes |
Yes |
|
GDEmenus version
2.5 09-05-14 |
NA |
Yes |
|
Highlight Helix |
Yes |
Yes |
|
Import Chromat Sequence |
Yes |
Yes |
|
Import Foreign Format |
Yes |
Yes |
|
LifeTrace Basecalling and Chromat Viewer |
Yes |
Yes |
|
Loop Tool |
Yes |
Yes |
|
MacGDE Program Updated
09-05-14 |
Yes |
NA |
|
Make Consensus |
Yes |
Yes |
|
MFold 3.2 (Web server) |
Yes |
Yes |
Motif Search |
Yes |
Yes Protein |
Mr. Bayes 3.2.1 (Intel) 3.1.2 (PPC) Updated 09-05-14 |
Yes |
Yes |
|
Parallel Mr. Bayes 3.2.1 (Intel) 3.1.2 (PPC) Updated 09-05-14 |
Yes |
Yes |
|
MRTRANS (BIRCH Package) cDNA alignment from Amino Acids |
Yes |
Yes |
|
ModelTest 3.7 Requires
PAUP* |
Yes |
Yes |
|
MUSCLE 3.8.31 Added 09-05-14 |
Yes |
Yes |
|
MView |
Yes |
Yes |
|
NASTAT (BIRCH Package) nucleic acid freq. |
Yes |
Yes |
|
Open Reading Frame (ORF) GenBank |
NA |
Yes |
|
PAUP* See
NOTES 1 and 2 Below |
No |
Yes |
|
Phylip 3.69 Updated 09-05-14 |
Yes |
Yes |
|
PhyML
2.4.5 |
Yes |
Yes |
|
PhyML
3.0 |
Yes |
Yes |
|
PRIMER 3 rel. 1.0 Local
and Web |
Yes |
Yes |
|
PROT2NUC (BIRCH Package) Reverse Translate |
Yes |
Yes |
|
ProtTest 2.4 Updated 09-05-14 |
Yes |
Yes |
|
RAxML 7.3.0 (Intel Only) Added 09-05-14 |
Yes |
Yes |
|
ReadSeq (Import/Export) Updated 09-05-14 |
Yes |
Yes |
|
Restriction sites |
Yes |
Yes |
|
REFORM (BIRCH Package) |
Yes |
Yes |
|
Sort |
Yes |
Yes |
|
TACG ver 2.35f |
Yes |
Yes |
|
T-Coffee 3.84 |
Yes |
Yes |
|
Translate |
Yes |
Yes |
|
TreeTool
2.0.2 |
Yes |
Yes (in Phylogeny choices) |
|
TreeView
X 0.5 and Classic 1.6.6 |
Yes |
Yes (in Phylogeny choices) |
|
VecScreen GenBank |
NA |
Yes |
Note3: Please register yourself with the individual programs authors to be informed of updates.