EXPEYES(1) expEYES User Manual EXPEYES(1)NAME
expEYES - an interactive board to control the ExpEYES box
SYNOPSIS
expEYES
DESCRIPTION
expEYES is a program to control interactlively most features of the ExpEYES box.
ExpEYES is from the PHOENIX project of Inter-University Accelerator Centre, New Delhi. It is a hardware & software framework for developing
science experiments, demonstrations and projects and learn science and engineering by exploration. Capable of doing real time measurements
and analysing the data in different ways. Analog voltages are measured with 0.025% resolution and time intervals with one microsecond. This
project is based on Free and Open Source software, mostly written in Python programming language. The hardware design is also open.
AUTHOR
Georges Khaznadar <georgesk@ofset.org>
Wrote this manpage for the Debian system.
COPYRIGHT
Copyright (C) 2011 Georges Khaznadar
This manual page was written for the Debian system (and may be used by others).
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at
your option) any later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
expEYES 04/19/2011 EXPEYES(1)
Check Out this Related Man Page
POPULATIONS(1) populations User Manual POPULATIONS(1)NAME
populations - population genetic software
SYNOPSIS
populations
populations [name_of_input_file] [option]
You can use populations as a command line programm (very useful for batch treatment) to infer phylogenetic trees.
DESCRIPTION
populations is a population genetic software. It computes genetic distances between populations or individuals. It builds phylogenetic
trees (NJ or UPGMA) with bootstrap values.
FEATURES
o haploids, diploids or polyploids genotypes (see input formats)
o structured populations (see input files structured populations
o No limit of populations, loci, alleles per loci (see input formats)
o Distances between individuals (15 different methods)
o Distances between populations (15 methods)
o Bootstraps on loci OR individuals
o Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)
o Allelic diversity
o Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)
OPTIONS -phylogeny ind|pop
(default) for phylogenetic trees based on individuals or populations
dist method
(default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances
for details.
-construct method
(default: upgma) possibilities upgma or nj (Neighbor Joining)
-bootstrap_ind n
number to indicate the number of bootstraps to perform on individuals
-bootstrap_locus n
number to indicate the number of bootstraps to perform on loci
.RE
-output name_of_treeview_file
to indicate the name of the tree file (phylip tree format)
-level n
number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is
2...).
EXAMPLE
populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre
Commands can be write in a .bat file (for DOS) or a script file (for UNIX)
AUTHOR
Georges Khaznadar <georgesk@ofset.org>
Wrote this manpage for the Debian system.
COPYRIGHT
Copyright (C) 2011 Georges Khaznadar
This manual page was written for the Debian system (and may be used by others).
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at
your option) any later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
populations 06/19/2011 POPULATIONS(1)