General Tools:

Text editor, emacs , Notepad++ - use these for manipulate txt files for sequences, scripts, matrices, etc.

Filezilla for transfering files between your laptop and a (Linux) server. Instrcutions on how to setup the client for HiPerGator.

putty for connecting to HiPerGator from a Windows PC (MacOS comes with Terminal)

Bioinformatics Softwares:

BLAST: Read the BLAST Manual before you download and install the  Blast executables (this one is for MS Windows OS)

BaGua.exe for identifying patterns.  You will need to name the dataset (containing FASTA formated sequences) as "dfile.txt" in the same folder.  An example of pattern will be MA[DE]XX[^LI].  

DotPlot:  Download the Dotplot-2.0 or the WinDot zipfile, unzip the contents into a folder named "Dotplot" or "windot".  double click the dotplot.exe or windot.exe icon to activate the program. 

Comprehensive protein analysis tool JalView : Sequence retrieval; alignment, phylogentic tree, structure,etc.

Sequence Sets: