.\" 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 DESCPOLY 1 "Jun 3, 2003" .\" 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 descPoly \- a program to qualitatively describe features of polymorphism data .SH SYNOPSIS .B descPoly -i -o .RI [ options ] .SH DESCRIPTION \fBdescPoly\fP prevides a description of sequence polymorphism data. The main purpose of the program is to describe "oddities" that are normally ignored in analysis. These include: sites with multiple hits, gaps, SNPs over gaps, and sites with missing data. .PP .SH OPTIONS \fBdescPoly\fP accepts the following options: .TP .B \-i specify a file containing aligned sequences in FASTA format to analyze .TP .B \-o specify the outgroup sequence in the data. The value input is an index. For example, if the first sequence in the infile is the outgroup, pass the value 0 to the program .\" .SH "SEE ALSO" .\" .BR foo (1), .\" .BR bar (1). .SH AUTHOR Kevin Thornton