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NCLconverter

NCLconverter is a file conversion utility. It reads in a file in a recognized format, and writes the chosen output format. We have found it to be more robust than the Readseq parser, especially for large phylogenetic files. Mixed data types (for example, DNA, RNA, and protein in a single matrix) are not currently supported. This utility was created from the Nexus Class Library.

When parsing NEXUS files, NCLconverter allows the user to specify the strictness level. The default level is equivalent to s = 2. Using s = 3 or a higher number will convert some warnings into fatal errors. Running with s = 1 will cause the parser to accept "dangerous" constructs, and running with s = 0 will cause the parser make every attempt to finish parsing the file (warning about very serious errors). When s = 0 strictness level is used, the parser often fails to finish because of an error that precedes the error reported.

INPUT= The converter accepts the following files as input types: Nexus, Fasta (DNA, RNA, Amino Acid), Clustal (DNA, RNA, Amino Acid) Phylip (DNA, RNA, Amino Acid, Discrete chars), interleaved or non-interleaved, Relaxed Phylip (DNA, RNA, Amino Acid, Discrete chars), interleaved or non-interleaved, Newick (Phylip Tree), strict or relaxed; and NEXML.

OUTPUT = The converter can create the following output formats:

"normalized" NEXUS output. Normalization of Nexus is a concept intended to conform the highly variable Nexus format types into a format that can be managed reliably by most tools and parsers. See here.
fasta: Character data in fasta (could result in multiple output files),
Phylip: phylipTrees and character data in phylip (could result in multiple output files)
Relaxedphylip Trees and character data in relaxed phylip (could result in multiple output files)
Nexml output (this is also the default

KNOWN ISSUE: The "normalized" Nexus created by this parser will not be usable by MrBayes 3.1. The reason is that "normalized" Nexus has separate character and taxon elements; MrBayes 3.1 requires these two parameters to be combined into a single element called Data.

Test input file (Nexus format): nclconverter_in.txt

Test output file (NEXML format): nclconverter_out.txt (Note: Microsoft Internet Explorer may not open this file properly, but other browsers succeed. If you use MSIE, you can right click on the link and download the file to view it.

NCLconverter can be found at:

Lewis, P.O., and Holder, M. T. (2008) Nexus Class Library, http://sourceforge.net/projects/ncl/.

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