Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index e2f013d..503fc75 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -43,7 +43,11 @@ msa.each do |entry|
 end
 }}}
 
- 
+Relevant API documentation:
+
+ * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]
+ * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
+ * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
 
 === Writing a Multiple Sequence Alignment to a File ===
 
@@ -67,7 +71,7 @@ The following symbols determine the output format:
 
   * `:clustal` for ClustalW
   * `:fasta` for FASTA
-  * `:phylip`for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
+  * `:phylip` for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
   * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
   * `:msf` for MSF
   * `:molphy` for Molphy
@@ -82,8 +86,6 @@ f.write(align.output(:phylipnon))
 
 === Formatting of Individual Sequences ===
 
-_... to be done_
-
 !BioRuby can format molecular sequences in a variety of formats.
 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
 
@@ -97,9 +99,16 @@ For Bio::!FlatFile entries:
 entry.to_biosequence.output(:genbank)
 }}}
 
-The following symbols determine the output format.
-  *`:genbank` for Genbank
-
+The following symbols determine the output format:
+  * `:genbank` for Genbank
+  * `:embl` for EMBL
+  * `:fasta` for FASTA
+  * `:fasta_ncbi` for NCBI-type FASTA
+  * `:raw` for raw sequence
+  * `:fastq` for FASTQ (includes quality scores)
+  * `:fastq_sanger` for Sanger-type FASTQ 
+  * `:fastq_solexa` for Solexa-type FASTQ 
+  * `:fastq_illumina` for Illumina-type FASTQ 
 
 == Calculating Multiple Sequence Alignments ==