Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 622deb1..503fc75 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -13,17 +13,17 @@ 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 Alignments =
+= Multiple Sequence Alignment =
 
 
 == Multiple Sequence Alignment Input and Output ==
 
 === Reading in a Multiple Sequence Alignment from a File ===
 
-The follow example shows how to read in a *ClustalW*-formatted multiple sequence alignment.
+The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment.
 
 {{{
 #!/usr/bin/env ruby
@@ -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 ===
 
@@ -63,23 +67,48 @@ 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))
 }}}
 
 
+=== Formatting of Individual Sequences ===
+
+!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.
+
+For Sequence objects:
+{{{
+seq.to_seq.output(:genbank)
+}}}
+
+For Bio::!FlatFile entries:
+{{{
+entry.to_biosequence.output(: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 ==
 
@@ -237,6 +266,15 @@ tree = trees[3]
 }}}
 
 
+====Nexus  Format====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
 
 === Writing of Phylogenetic Trees ===
 
@@ -279,18 +317,28 @@ writer.write(tree2)
 }}}
 
 
+====Nexus  Format====
 
-== Phylogenetic Inference ==
+_... to be done_
 
-_Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastME..._
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
 
-_What about pairwise distance calculation?_
 
+= Phylogenetic Inference =
 
+_Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastME..._
 
-== Maximum Likelihood ==
+== Optimality Criteria Based on Character Data ==
 
-=== RAxML ===
+Character data based methods work directly on molecular sequences and thus do not require the calculation of pairwise distances but tend to be time consuming and sensitive to errors in the multiple sequence alignment.
+
+=== Maximum Likelihood ===
+
+==== RAxML ====
 
 _... to be done_
 
@@ -301,7 +349,7 @@ require 'bio'
 }}}
 
 
-=== PhyML ===
+==== PhyML ====
 
 _... to be done_
 
@@ -311,9 +359,45 @@ require 'bio'
 
 }}}
 
+=== Maximum Parsimony ===
+
+Currently no direct support in !BioRuby.
+
+
+=== Bayesian Inference ===
+
+Currently no direct support in !BioRuby.
+
+
 == Pairwise Distance Based Methods ==
 
-=== FastME ===
+=== Pairwise Sequence Distance Estimation ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+=== Optimality Criteria Based on Pairwise Distances ===
+
+
+==== Minimal Evolution: FastME ====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+=== Algorithmic Methods Based on Pairwise Distances ===
+
+==== Neighbor Joining and Related Methods ====
 
 _... to be done_
 
@@ -325,7 +409,7 @@ require 'bio'
 
 
 
-=== PHYLIP? ===
+