=== Writing a Multiple Sequence Alignment to a File ===
-The follow example shows how to writing a multiple sequence alignment in *Fasta*-format:
+The follow example shows how to writing a multiple sequence alignment in *FASTA*-format:
{{{
#!/usr/bin/env ruby
The following constants determine the output format
* ClustalW: `:clustal`
- * Fasta: `:fasta`
- * Phylip interleaved: `:phylip`
- * Phylip non-interleaved: `:phylipnon`
+ * FASTA: `:fasta`
+ * PHYLIP interleaved (will truncate sequence names to no more than 10 characters): `:phylip`
+ * PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters): `:phylipnon`
* MSF: `:msf`
* Molphy: `:molphy`
-For example, the following writes in Phylip's non-interleaved format:
+For example, the following writes iPHYLIP's non-interleaved format:
{{{
f.write(align.output(:phylipnon))
}}}
+
== Calculating Multiple Sequence Alignments ==
!BioRuby can be used to execute a variety of multiple sequence alignment