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 =
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 ===
==== 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 ===
-_... 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.
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 ==