[Bioperl-guts-l] bioperl-live/doc/howto/txt Beginners.txt, 1.4, 1.5 PopGen.txt, 1.3, 1.4

[Brian Osborne]

Update of /home/repository/bioperl/bioperl-live/doc/howto/txt
In directory pub.open-bio.org:/tmp/cvs-serv28340/txt

Modified Files:
	Beginners.txt PopGen.txt 
Log Message:
New versions


Index: Beginners.txt
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RCS file: /home/repository/bioperl/bioperl-live/doc/howto/txt/Beginners.txt,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Beginners.txt	9 Sep 2005 00:23:11 -0000	1.4
--- Beginners.txt	4 Oct 2005 00:42:36 -0000	1.5
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*** 783,793 ****
     these are good values in principle there are no commonly agreed upon
     standard names - perhaps someday the authors will be able to rewrite
!    the code when we all agree what these values should be. Finally, you
!    may be wondering why the method names are what they are and why
!    particular fields or identifiers end up associated with particular
!    methods. Again, without having standard names for things that are
!    agreed upon by the creators of our public databases all the authors
!    could do is use common sense, and these choices seem to be reasonable
!    ones.
  
     Next let's take a look at the values returned by the methods used by
--- 783,793 ----
     these are good values in principle there are no commonly agreed upon
     standard names - perhaps someday the authors will be able to rewrite
!    the code when all our public databases agree what these values should
!    be. Finally, you may be wondering why the method names are what they
!    are and why particular fields or identifiers end up associated with
!    particular methods. Again, without having standard names for things
!    that are agreed upon by the creators of our public databases all the
!    authors could do is use common sense, and these choices seem to be
!    reasonable ones.
  
     Next let's take a look at the values returned by the methods used by
***************
*** 943,947 ****
  
     As in the Genbank example there's information that the Sequence object
!    doesn't supply, and it's stored in Annotation objects. See the
     [99]Feature and Annotation HOWTO for more.
  
--- 943,947 ----
  
     As in the Genbank example there's information that the Sequence object
!    doesn't supply, and it's all stored in Annotation objects. See the
     [99]Feature and Annotation HOWTO for more.
  
***************
*** 951,959 ****
     [100]Bioperl. Typically this means you have a means to run the program
     and frequently a means of parsing the resulting output, or report, as
!    well. Certainly the most popular analytical program is [101]BLAST, so
!    let's use it as an example. First you'll need to get BLAST, also known
!    as blastall, installed on your machine and running. This example also
!    assumes that you used the formatdb program to index the database
!    sequence file "db.fa".
  
     As usual, we start by choosing a module to use, in this case
--- 951,960 ----
     [100]Bioperl. Typically this means you have a means to run the program
     and frequently a means of parsing the resulting output, or report, as
!    well. Certainly the most popular analytical program is BLAST so let's
!    use it as an example. First you'll need to get BLAST, also known as
!    blastall, installed on your machine and running and versions of the
!    program that can run on all the popular operating systems can be
!    downloaded from [101]NCBI. The example code assumes that you used the
!    formatdb program to index the database sequence file "db.fa".
  
     As usual, we start by choosing a module to use, in this case
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*** 1324,1328 ****
    99. http://bioperl.org/HOWTOs/html/Feature-Annotation.html
   100. http://bioperl.org/
!  101. http://www.ncbi.nlm.nih.gov/BLAST/
   102. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/StandAloneBlast.html
   103. http://bioperl.org/HOWTOs/html/SearchIO.html
--- 1325,1329 ----
    99. http://bioperl.org/HOWTOs/html/Feature-Annotation.html
   100. http://bioperl.org/
!  101. http://www.ncbi.nlm.nih.gov/BLAST/download.shtml
   102. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/StandAloneBlast.html
   103. http://bioperl.org/HOWTOs/html/SearchIO.html

Index: PopGen.txt
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RCS file: /home/repository/bioperl/bioperl-live/doc/howto/txt/PopGen.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** PopGen.txt	9 Sep 2005 00:23:11 -0000	1.3
--- PopGen.txt	4 Oct 2005 00:42:36 -0000	1.4
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*** 54,59 ****
     sequence distance based calculations. A full treatment of the Bioperl
     interface to the PAML suite (Z.Yang, 1997) is covered in the [12]PAML
!    HOWTO> and objects and data pertinent to phylogenetic data
!    manipulation are covered in the [13]Trees HOWTO.
  
  2. The Bio::PopGen Objects
--- 54,59 ----
     sequence distance based calculations. A full treatment of the Bioperl
     interface to the PAML suite (Z.Yang, 1997) is covered in the [12]PAML
!    HOWTO and objects and data pertinent to phylogenetic data manipulation
!    are covered in the [13]Trees HOWTO.
  
  2. The Bio::PopGen Objects