Cipres Science Gateway | Format Validator Information

Format Validator

FormatValidator is a parsing tool created by Paul Lewis for the NCL tool. It was extracted into a standalone matrix format-checking tool by Mark Holder for this project. It can validate the following formats: Nexus; Fasta (DNA, RNA, and Protein); and Phylip, interleaved or not, relaxed or not, for DNA RNA Protein and Characters). The level of strictness is set using an integer parameter.

Reference: Lewis, P. O.(2003) NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics 19 (17): 2330-2331.

INPUT = any text file in Nexus; Fasta (DNA, RNA, and Protein); and Phylip, interleaved or not, relaxed or not, for DNA RNA Protein and Characters)dna or protein sequences in multiple fasta format (MFA).

OUTPUT = a report on the any format errors in the file.

Test input file (Nexus; correct): format_validator_infile_noerrors.nex

Test output file: (Nexus, correct): STDERR_output_noerrors.txt

Test input file (Nexus; correct): format_validator_infile_errors.nex

Test output file: (Nexus, correct): STDERR_output_errors.txt

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