After downloading ForCon, you have a .zip file. Unzip it using WinZip or PKUNZIP in a temporary directory. Double-click the setup.exe file and follow the instructions.
ForCon is a user-friendly software tool for the easy conversion of nucleic and amino acid sequence alignments into different formats.
At the moment, ForCon is able to convert ? in both ways, i.e. reading and writing - the
following formats (or formats used by the following software packages):
- CLUSTAL
- EMBL
- FASTA
- GCG/MSF
- Hennig86
- MEGA
- NBRF/PIR
- PAUP/Nexus
- Parsimony Jackknifer
- PHYLIP
- TREECON
Software packages not included in the list are usually able to read one of the formats mentioned. For the publication of sequence alignments, a format with codon positions can be generated ("Pretty").
Sequential and interleaved formats are supported by ForCon. (see next paragraph)
File formats
The use of correct formats is extremely important: incorrect formats cannot be correctly interpreted by the program. For this reason a description and example of all the formats is presented below.
Overall, two major types of formats exist: interleaved and noninterleaved (sequential). In the interleaved format, sequences are written in the form of an alignment: 
Usually the symbol for missing data is 'N' (nucleotides) or 'X' (proteins). For insertions/deletions ('gaps') the most commonly used symbol is a hyphen '-'.
