[FAQ] Welcome to FaBox (1.41) - an online fasta sequence toolbox
 

Sequence 2 fasta converters (external tools) HCV Sequence Conversion Interface - ReadSeq at EBI

Working with fasta headers
Fasta header extractor (and header splitter) Simple and fast way of extraction the headers from fasta files - and optionally split each header into fields based on a chosen character/word.
Fasta header editor Simple and fast way of extracting headers, edit them and reapplying them without worrying about the sequence itself.
Fasta header replacer Some programs do not like the fancy headers in fasta files and you have to live with short, unique names - that are really non-descriptive. Here you can replace headers back and forth by submitting old and new headers - which you'll typically keep in a excel spreadsheet.

Working with fasta datasets/alignments
Fasta sequence extractor Simple and fast way of extracting some sequences from a large sequence set, based on a list of headers or fuzzy matching.
Fasta sequence subtractor Simple and fast way of removing some sequences from a large sequence set, based on a list of headers or fuzzy matching.
Fasta sequence joiner Simple and fast way of joining a set of fasta sequences into one sequence
Fasta dataset splitter/divider Simple and fast way of dividing your dataset into two sets by a header keyword. It will split into sets WITH and WITHOUT the given header keyword (like 'females/males', 'population1/population2')
Fasta alignment joiner Simple and fast way of joining two alignments, sequence by sequence. It will join alignment 1,sequence 1 with alignment 2, sequence 1 and so on.... (see example)
Alignment trimmer Trims an alignment to the shortest sequence. It simply removes the boundary areas that are full of gaps.
Show variable sites only Extracts all the variable sites from an alignment
DNA to haplotype collapser and converter Will collapse a set of sequences into haplotypes and output som simple statistics and formatted input files for Arlequin

Data conversion
Strip branch lengths and bootstrap values from newick trees (newick parser) Will take a newick tree and create three versions: the original, branch lengths only and topology only (for ASR in paml).
Create formatted sequence file for PAML analysis (fasta2paml) Will format your fasta sequences and create a correct input file for PAML (it's a phylip format with some modifications).
Fasta2excel converter Will explode a sequence set into tabular format. It's possible to explode sequences base-by-base and to transpose (flip) the resulting table.
Create TCS input file from fasta (fasta2tcs) Will format your fasta sequences and create a correct input file for the TCS software (TCS: Phylogenetic network estimation using statistical parsimony, Clement et al. 2000).
Create Migrate input file from fasta (fasta2migrate) Will format your DNA sequences and create a migrate file called 'infile'. The produced file will be correctly formatted to be analysed by migrate.
Create MrBayes input file from fasta (fasta2mrbayes) Will format your DNA sequences and create a MrBayes file, with data and analysis settings included. The produced file will run a series of analyses and produce consensus trees with posterior probabilities.
DNA to haplotype collapser and converter Will collapse a set of sequences into haplotypes and output som simple statistics and formatted input files for Arlequin

Sequence generation
Random DNA sequence generator Generates a specified number of random DNA sequences of given length and exact base composition (will also generate sequences of varying length)