.\" hey, Emacs: -*- nroff -*- .\" analysis is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 2 of the License, or .\" (at your option) any later version. .\" .\" This program is distributed in the hope that it will be useful, .\" but WITHOUT ANY WARRANTY; without even the implied warranty of .\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the .\" GNU General Public License for more details. .\" .\" You should have received a copy of the GNU General Public License .\" along with this program; see the file COPYING. If not, write to .\" the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA. .\" .TH SHAREDPOLY 1 "Jun 3, 2002" .\" Please update the above date whenever this man page is modified. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins (default) .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME sharedPoly \- calculate the number of shared, private, and fixed polymorphisms between 2 partitions of aligned sequence data .SH SYNOPSIS .B sharedPoly -i -n .RI [ options ] .SH DESCRIPTION \fBsharedPoly\fP outputs the number of shared, private, and fixed differences between 2 partitions of aligned sequence data. This may be useful if data are sampled from 2 populations or duplicated genes. .PP .SH OPTIONS \fBsharedPoly\fP accepts the following options: .TP .B \-i specify a file containing aligned sequences in FASTA format to analyze .TP .B \-n nsam1 is the number of sequences in the first partition. For example, if there are 10 sequences in the file, 6 from population 1, and 4 from population 2, pass \-n 6 to the program. .TP .B \-v verbose output .\" .SH "SEE ALSO" .\" .BR foo (1), .\" .BR bar (1). .SH AUTHOR Kevin Thornton