Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 0c3686c..503fc75 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -13,7 +13,7 @@ Eventually, this is expected to be placed on the official !BioRuby page.
 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
 
  
-Copyright (C) 2011 Christian M Zmasek
+Copyright (C) 2011 Christian M Zmasek. All rights reserved.
 
 
 = Multiple Sequence Alignment =
@@ -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 ===
 
@@ -63,17 +67,17 @@ end
 
 ==== Setting the Output Format ====
 
-The following constants determine the output format.
+The following symbols determine the output format:
 
-  * 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`
+  * `:clustal` for ClustalW
+  * `:fasta` for FASTA
+  * `: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
 
 
-For example, the following writes PHYLIP's non-interleaved format:
+For example, the following writes in PHYLIP's non-interleaved format:
 
 {{{
 f.write(align.output(:phylipnon))
@@ -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)
 }}}
 
-Constants for available formats are:
-  * Genbank :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 ==
 
@@ -364,12 +373,27 @@ Currently no direct support in !BioRuby.
 
 === Pairwise Sequence Distance Estimation ===
 
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
 
-=== Optimality Criteria Based Methods ===
+=== Optimality Criteria Based on Pairwise Distances ===
 
 
 ==== Minimal Evolution: FastME ====
 
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
 
 === Algorithmic Methods Based on Pairwise Distances ===