repeatoire(1)
NAME
repeatoire - part of mauveAligner package
DESCRIPTION
Allowed options:
--allow-redundant arg (=1)
allow redundant alignments?
--chain arg (=1)
chain seeds?
--extend arg (=1)
perform gapped extension on chains?
--window arg (=-1)
size of window to use during gapped extension
--gapopen arg (=0)
gap open penalty
--gapextend arg (=0)
gap extension penalty
--h arg (=0.00800000038)
Transition to Homologous
--help get help message
--highest arg (=procrast.highest) file containing highest scoring
alignment
for each multiplicity
--l arg (=1)
minimum repeat length
--large-repeats arg (=0)
optimize for large repeats
--load-sml arg (=0)
try to load existing SML file?
--onlydirect arg (=0)
only process seed matches on same strand?
--onlyextended arg (=0)
only output extended matches?
--output arg
procrastAligner output
--percentid arg (=0)
min repeat family % id
--novel-subsets arg (=0)
find novel subset matches?
--novel-matches arg (=1)
use novel matches found during gapped extension?
--rmax arg (=500)
maximum repeat multiplicity (max copy number)
--rmin arg (=2)
minimum repeat multiplicity (min copy number)
--seeds arg
seed output file
--sequence arg
FastA sequence file
--small-repeats arg (=0)
optimize for small repeats
--score-out arg
output with corresponding score and alignment info
--solid arg (=0)
use solid/exact seeds?
--sp arg (=0)
minimum Sum-of-Pairs alignment score
--tandem arg (=1)
allow tandem repeats?
--two-hits arg (=0)
require two hits within w to trigger gapped extension?
--u arg (=0.00100000005)
Transition to Unrelated
--unalign arg (=1)
unalign non-homologous sequence?
--w arg (=0)
max gap width
--xmfa arg
XMFA format output
--xml arg
XML format output
--z arg (=0)
seed weight
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
