Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 0a244d5..91baa22 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -48,7 +48,7 @@ end
 === 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
@@ -63,21 +63,22 @@ end
 
 The following constants determine the output format
 
-  * ClustalW: '`:clustal`'
-  * Fasta:    '`:fasta`'
-  * Phylip interleaved: '`:phylip`'
-  * Phylip non-interleaved: '`:phylipnon`'
-  * MSF: '`:msf`'
-  * Molphy: '`:molphy`'
+  * ClustalW: `:clustal`
+  * 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