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File xtandem.1 of Package xtandem
.\" -*- nroff -*- .\" .Dd February 5, 2013 .Dt XTANDEM 1 .Os .Sh NAME .Nm xtandem .Nd X! Tandem Spectrum Modeler .Sh SYNOPSIS .Nm xtandem .Bk -words .Ar input.xml .Ek .Sh DESCRIPTION X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. .Pp This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. .Sh FILES .Bl -tag -compact -width Ds .It Pa /usr/share/xtandem Directory containing sample input and configuration files .It Pa /usr/share/xtandem/fasta Directory containing database files .It Pa /usr/share/xtandem/xsl HTML stylesheets for viewing input and output files .El .Sh SEE ALSO .Rs .%T "X! Tandem Spectrum Modeler" .%O http://www.thegpm.org/TANDEM/instructions.html .Re .Rs .%T "X! Tandem Database Files" .%O ftp://ftp.thegpm.org/fasta/ .Re
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