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CarbonFolder

Free - NeoWise Software
CarbonFolder is a fast and easy in use data synchronization utility, which allows the user to synchronize data in different folders located in home PC and local network. The utility features a simple interface designed as a step-by-step wizard, which is clear to anyone and lets users perform synchronization in seconds. What’s more, the program saves any newly created task for the next launch. Supports Windows 98/Me/NT/2000/2003/XP/Vista.
folders, rename, files, batch, folder, file, replace, directory, convert, renamer, windows, icon
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File Renamer Basic

Free - Sherrod Computers, Inc.
File Renamer Basic is a powerful and yet easy to use program that allows the user to rename files, folders, and MP3 files with ease. It has a filename filter so you can easily narrow down your search to only a specifc type of file or filename to work with. You can also remove x number of characters starting from x character and even find and replace text. In addition to its renaming capabilities, it also has a built-in ID3v1 and ID3v2 tag editor.
exif, jpeg, download, explorer, create, conversion, password protect, file rename, multi fasta, multifasta, fasta, format
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Advanced Renamer

Free - Hulubulu Software
Advanced Renamer is freeware program for naming a large batch of files or folders in a snap. It uses several methods for creating the new names and it has tools for multimedia files like photo and music files. With Advanced Renamer you can construct new file names by adding, removing, replacing, changing case, or giving the file a brand new name based on known information from the file.
directories, image, delete, case, proportion, caller, code, nucleotide, codone, phred, file format, sequence
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File Renamer

Free - Jose Falcao
File Renamer will let you rename all your files and folders, but with a lot more options. Can batch rename files, add or remove strings to filenames, change file extensions, numerate filenames sequentially, convert to uppercase or lowercase, trim characters, replace strings, and some more.. Works with multiple directories, suports Drag and Drop and works from the command line. Also has 'undo' function for past renames done.
assembly, base, align, number, between, basecaller, multimedia, pictures, naming, renaming, shortcuts, manager
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ID3 renamer

Free - x2develop.com
Useful if you need to rename a large number of files in a directory accordingly to their ID3 description and a given "formula" (e.g. (%Track) %Artist - %Title). Such a function is pretty "smart", as it lets you assembly the filename as you wish and use the variables from the ID3 tag in the filename. You can also fill ID3 tag with some smart functions.
tray, windows explorer, drive, hotkey, 32bit, 32 bit, system, custom, 2000, customise, shift, support
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FASTA to multi-FASTA converter

Free - HeracleSoftware
www.DNABaser.com
This tool will look for all DNA FASTA files in the specified folder and will merge their content in a single file. The output file is automatically saved on the HDD.
Other software:
DNA Baser is an affordable alternative for assembly of DNA sequences and generation of contigs. File formats supported are abi, scf and seq (or FASTA). Chromatograms of the assembled sequences are displayed in a synchronized format with the generated contig.
shell, colorizer, customize, arcticline, change, desktop, foldermarker, colorize, windows 9x, settings, folder color, name
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