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Start Your TrialNCLconverter 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.
Supported parameters:
toolId=NCLCONVERTER
input.infile_ - Primary Input File
vparam.runtime_ - Float - Maximum Hours to Run (up to 168 hours) (default=1.0)
vparam.format_type_ - Excl -Choose the Input Format. nexus (default), fasta, phylip, phylipt, clustal, nexml
vparam.data_type_ - Excl - Specify the Data Type (Mixed data types are not supported) dna (default), rna, protein, discrete
vparam.relaxed_type_ - Switch - >My data is in a relaxed Phylip format (default=0)
vparam.interleaved_type_ - Switch - My data is interleaved (default=0).
vparam.nexus_strictness_ - Integer - Set the NEXUS strictness level (-s). (default=2)
vparam.output_type_ - Excl - Choose the Output format (* values could produce multiple output files) -enexus (default), -efasta, -ephylip, -erelaxedphylip, -enexml
vparam.outfile_nexus_ = String - Please enter a prefix for your output file (default is "out") (no default)