From f88ebacb73d58626afcff3e711876eb39bd15994 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 1 Mar 2011 03:19:31 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 847b552..3e40347 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -48,7 +48,7 @@ end === Writing a Multiple Sequence Alignment to a File === -The follow example shows how to writing a multiple sequence alignment in *Fasta*-format: +The follow example shows how to writing a multiple sequence alignment in *FASTA*-format: {{{ #!/usr/bin/env ruby @@ -64,20 +64,21 @@ end The following constants determine the output format * ClustalW: `:clustal` - * Fasta: `:fasta` - * [http://evolution.genetics.washington.edu/phylip.html PHYLIP] interleaved: `:phylip` - * [http://evolution.genetics.washington.edu/phylip.html PHYLIP] non-interleaved: `:phylipnon` + * FASTA: `:fasta` + * PHYLIP interleaved: `:phylip` (will truncate sequence names to no more than 10 characters) + * PHYLIP non-interleaved: `:phylipnon` (will truncate sequence names to no more than 10 characters) * MSF: `:msf` * Molphy: `:molphy` -For example, the following writes in [http://evolution.genetics.washington.edu/phylip.html PHYLIP]'s non-interleaved format: +For example, the following writes iPHYLIP's non-interleaved format: {{{ f.write(align.output(:phylipnon)) }}} + == Calculating Multiple Sequence Alignments == !BioRuby can be used to execute a variety of multiple sequence alignment -- 1.7.10.2