There are many different formats for storing alignments in files.
Formats that can be read by many (but not all) phylogenetic software include:
- fasta
- nexus (which can be used to store much more than just alignment data)
- phylip (both interleaved and sequential)
To convert from fasta to phylip format you could use:
- Phylogeny.fr data converter (works going from fasta to phylip interleaved for use by PhyML)
- ClustalX