X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=503fc75198d7b5b23435fd2e6b5ea0e23cab9a8c;hb=e49430be142b9b3d380b87d7040b4664e3174644;hp=44136a654f67c20a3b4c1b0f0b54a27345d076d9;hpb=bacc8852471ae415fe71942d006671f8ead35e4f;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 44136a6..503fc75 100644
--- 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 ===
 
@@ -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.
 
@@ -101,14 +103,12 @@ The following symbols determine the output format:
   * `:genbank` for Genbank
   * `:embl` for EMBL
   * `:fasta` for FASTA
-  * `:fasta_ncbi` for 
-  * `:raw` for
-  * `:fastq` for
-  * `:fastq_sanger` for
-  * `:fastq_solexa` for
-  * `:fastq_illumina` for
-  * `:fasta_numeric` for
-  * `:qual` for
+  * `: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 ==