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