From: cmzmasek@gmail.com Date: Tue, 1 Mar 2011 20:17:53 +0000 (+0000) Subject: Edited wiki page PhyloBioRuby through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f258534e02445f65979c159c7ee01d5112b3f978;p=jalview.git Edited wiki page PhyloBioRuby through web user interface. --- diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 0b07ebe..cc63cfd 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -16,12 +16,12 @@ Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical R Copyright (C) 2011 Christian M Zmasek -= Multiple Sequence Alignments = +=1 Multiple Sequence Alignments = -== Multiple Sequence Alignment Input and Output == +==1.1 Multiple Sequence Alignment Input and Output == -=== Reading in a Multiple Sequence Alignment from a File === +===1.1.1 Reading in a Multiple Sequence Alignment from a File === The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment. @@ -45,7 +45,7 @@ end -=== Writing a Multiple Sequence Alignment to a File === +===1.1.2 Writing a Multiple Sequence Alignment to a File === The following example shows how to write a multiple sequence alignment in *FASTA*-format. It first creates a file named "outfile.fasta" for writing ('w') and then writes the multiple sequence alignment referred to by variable 'msa' to it in FASTA-format (':fasta'). @@ -61,7 +61,7 @@ File.open('outfile.fasta', 'w') do |f| end }}} -==== Setting the Output Format ==== +====1.1.2.1 Setting the Output Format ==== The following constants determine the output format. @@ -80,7 +80,7 @@ f.write(align.output(:phylipnon)) }}} -== Formatting of Individual Sequences == +===1.1.3 Formatting of Individual Sequences === _... to be done_