Free Knowledge Resources


Linux Manual Pages


Free Software * Books

Source Code

Free Media

Linux

probalign(1)


NAME

   probalign  - Align sequences in MFAFILE(s) and print result to standard
   output

DESCRIPTION

   PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences  and
   prints to the standard output. Written by Satish Chikkagoudar and Usman
   Roshan using code from PROBCONS version 1.1 (written by Chuong Do)  and
   based upon probA (written by Ulrike Muckstein).

   PROBALIGN  1.4  comes  with  ABSOLUTELY  NO  WARRANTY.   This  is  free
   software,  and  you  are  welcome  to  redistribute  it  under  certain
   conditions.  See the README file for details.

   Usage:
          probalign [OPTION]... [MFAFILE]...

   Description:
          Align  sequences  in  MFAFILE(s)  and  print  result to standard
          output

   -clustalw

          use CLUSTALW output format instead of MFA

   -v, --verbose

          report progress while aligning (default: off)

   -a, --alignment-order

          print sequences in  alignment  order  rather  than  input  order
          (default: off)

   -T, -temperature

          Sets the thermodynamic temperature parameter

          (default:  5  (for  protein  data mode), 1 ( for nucleotide data
          mode)).

   -score_matrix, --score_matrix

          Sets the type of scoring matrix used to calculate the  posterior
          probabilities  (default:  gonnet_160,  representing  gonnet 160,
          refer README for details)

   -go, --gap-open

          This option can be used to specify the gap open  parameter.  The
          default  for  Gonnet  160 (protein) is 22 and nucleotide (simple
          matrix) is 4.

   -ge, --gap-extension

          This option can be used to specify the gap extension  parameter.
          The default for Gonnet 160 (protein) is 1 and nucleotide (simple
          matrix) is 0.25.

   -nuc

          Specify this option to  indicate  that  inputted  sequences  are
          nucleotide sequences

   -prot

          Specify  this  option  to  indicate  that inputted sequences are
          protein sequences [DEFAULT]

   -showPP

          Outputs the posterior probabilities of alignment  columns  as  a
          new  sequence  named  Posterior  Probabilities  (The probability
          values are scaled to be between integers between 0 and 9).



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.


birds banner