GeneBank To FASTA

This tool takes a gene bank formatted file as input with one or more records.
It then concatenates the ID, AC, and DR values to form the FASTA header (>ID_AC_DR_DR_...).
Followed by whichever information is contained as a sequence (stripped from blanks, numbers and converted to upper case).
Download the zip file GeneBank2FASTA
The usage is as follows:
Unzip to a directory and open the console then point the console to the folder containing the .jar file.
Run in console:
java -jar GeneBankToFasta.jar INPUTFILEPATH OUTPUTFILEPATH
replace the PATH placeholders with a relative or absolute path to the input file and to where you want the output to be saved.

FASTA Splitter and Joiner

This tool allows splitting and joining of FASTA files. It will never split within a sequence.
Download the jar file FastaSplitterJoiner
Run in console:
java -jar FastaSplitterJoiner INPUTFILEPATH MODE(split/join) SIZE(bytes) OUTPUTFILEPATH (NUMCHARPERLINE)
replace the PATH placeholders with a relative or absolute path to the input file and to where you want the output to be saved.
Choose either split or join for MODE and specify the target file size in bytes.
Exp: java -jar FastaSplitterJoiner.jar c:\toSplit.fasta split 50000 c:\split
Note that for join mode INPUTFILEPATH needs to be a directory and not a file.
After joing all files in the directory you can easily split to the desired size.
The optional parameter 5 (NUMCHARPERLINE) specifies how many nucleotides/amino acids/characters should be on one sequence line.

Reads To FASTA

ACE to FASTA

This tool allows to convert CAP3 ace files into FASTA files.
Download the zip file c2f
Extract the file to any directory and you are ready to use Cap3ToFasta.
Run in console:
java -jar Cap3ToFasta.jar CAP3DIR OUTPUTDIR
Replace CAP3DIR with the path to where the cap3 results are stored (.ace files).
Replace OUTPUTDIR with the directory where you want the fasta files to be stored.
It can be the same directory.
Exp: java -jar Cap3ToFasta.jar c:\cap3output c:\fastaversions

Shuffle Sequence Order

This tool allows to ranomize the sequence in which sequences are organized
within a FASTA formated file of any size.
Download the zip file rfo
Extract the file to any directory and you are ready to use RandomizeFastaOrder.
Run in console:
java -jar RandomizeFastaOrder.jar INPUTFASTAFILE OUTPUTFASTAFILE
Replace INPUTFASTAFILE with the path to where the fasta formated file is located.
Replace OUTPUTFASTAFILE with the name of the file where you want the new file to be.
It cannot be the same file.
Exp: java -jar RandomizeFastaOrder.jar c:\input.fasta c:\shuffled.fasta