External packages 
I  haven't tried to install the external packages (AceDB, Blast, Clustalw, Tcoffee), or the XS based modules from bioperl-ext. 

PPM3 Installation of Bioperl:

Start PPM by typing 'ppm3' at the command prompt after entering the C:\Perl directory (You can also start it from program files->Active State->PPM). This gets you the 'PPM> ' prompt. You can now issue the following  commands:

if you are using PPM 3.0 beta release (comes with build 631 of perl 5.6) then do not add the trailing '/' to the repository urls and follow instructions in the next section to install bioperl. We dont store dependent modules with bioperl distributions and PPM 3 beta wants them all in one place.

rep add Bioperl http://bioperl.org/DIST/
rep add Temp http://wartik19.biotec.psu.edu/Bioperl/

search bioperl
and then
install [serial number of Bioperl-1.2 PPM3 archive]

If you see:

Writing C:\Perl\\site\lib\auto\bioperl\.packlist
Successfully installed Bioperl-1.2 version 1.2 in ActivePerl 5.6.1.633.

on your screen. You are all set!....enjoy bioperl!!

Caution:

• However if ppm cant find some dependent modules, you will get:
  'Cant locate <module-name>.ppd on <Location Name>' In that case follow the next section to install Bioperl.
• If all the dependencies are not listed then you may have to install the dependent modules one by one using search...<module name> and install ..<module name> on ppm.
• It is also safer to install the dependent modules manually because if the distribution of bioperl that you get on ppm doesnot have the dependencies listed you can be in trouble. You will see the "Successfully installed..." but trust me you are in trouble!. To avoid this-- Before installing bioperl (but after you 'search' for bioperl), type the following on PPM :

describe [package number in search] (if you see something like this:)

Name: Bioperl (or Bioperl-1.2)
Version: 1.2
Author: <Some Author>
Title: Bioperl
Abstract: Bioperl 1.2 PPM3 Archive
Location: <Some repository>
Prerequisites:
1. File-Temp 0.12
2. IO-String 1.0.1
3. IO-stringy 2.1
4. XML-Writer 0.4
5. XML-Node 0.11
6. XML-Twig 3.0.4
7. libxml-perl 0.0.7
8. DBD-mysql 2.1025
9. Graph 0.20101
10. GD 2.06
11. Text-Shellwords 1.0
Available Platforms:
1. MSWin32-x86-multi-thread

and the stuff in red is listed for the package you are trying to install, then you are fine. If there are no prerequisites listed then follow the next section and its steps to install bioperl correctly. Do Not install the bioperl package directly.

Text::Shellwords
PPM version is now available: If you dont get it on ppm, download the zip file from CPAN and the usuall
perl Makefile.pl, Nmake, Nmake test, Nmake install: Will work fine.

This module is not essential if you are going to install bioperl using PPM, its required only for running the tests
if you do the Makefile.pl, Nmake, Nmake test, Nmake install procedure for installing bioperl (see next section).

if you dont find some of the above modules on ppm, add the following repository:
repository add Winnipeg_server http://theoryx5.uwinnipeg.ca/ppmpackages/

and then repeat the search, install for the modules that you did not find then add the repositories for bioperl (if you havent done that already)

rep add Bioperl http://bioperl.org/DIST/
rep add Temp http://wartik19.biotec.psu.edu/Bioperl/
.....(now search for bioperl and install it).....
search bioperl
and then
install [serial number of Bioperl-1.2 PPM3 archive]

This time you dont have to worry about the archive listing the dependencies, because we have installed them manually beforehand. If you want to run the tests and do the install yourself in the old way...read on. Other wise you are all set!....enjoy bioperl!!

Tools 
Most perl modules are distributed tarred and gzipped, so you will need a program that can handle compressed files. WinZip ( www.winzip.com) works nicely for me. You will also need a make utility. Nmake seems to be the tool of choice on windows, and is freely available (http://download.microsoft.com/download/vc15/Patch/1.52/W95/EN-US/Nmake15.exe). Executing this self-extracting program generates the files readme.txt , nmake.err and nmake.exe. You can copy nmake.exe and nmake.err to a directory on your path, such as C:\WINNT\system32\ , or you can copy these two files into the directories from which you wil install bioperl and its dependencies. To verify which directories constitute your path, you can open a command prompt (a "DOS-box") from the start menu, and use the command 'path'.

Generated sub tests. go make show_tests to see available subtests
Do you want to run the BioDBGFF tests (requires a mysql database) y/n [n] (I said No)

External Module Ace, Aceperl, is not installed on this computer.
The Bio::DB::Ace in Bioperl needs it for access of ACeDB database
(This warns that Bio::DB::Ace is going to be useless without additional external   modules.)

...ends with
Writing Makefile for Bio

Nmake
This will simply set up the directory structure for testing and installing.
Nmake test

This will generate   lots of output, mostly just of the form 't\AAChange..........ok'.
Highlights   include:

• t\Assembly..........DB_File not installed. This means the Assembly modules are not available. Skipping tests.
• t\DB................ok, 1/78 skipped: unknown reason
• t\flat..............DB_File not loaded. This means flat.t test cannot be executed. Skipping
• t\game..............Subroutine _initialize redefined at C:/Downloads/bioperl-1.2/blib/lib/Bio\SeqIO\game.pm line 98.
  Subroutine _export_subfeatures redefined at C:/Downloads/bioperl-1.2/blib/lib/Bio\SeqIO\game.pm line 128.
  .
  .
  ends with ....
  Use of uninitialized value in print at C:\Perl\lib/IO/Handle.pm line 394.
  t\game..............ok

• Same thing happens for: t\phd...............ok, t\qual..............ok, t\scf...............ok, t\SearchIO..........ok
• t\SeqFeatCollection.DB_File not installed. This means the SeqFeatCollection wont work
• t\SeqIO.............ok, 3/146 skipped: unknown reason.

And  the final summary on my machine is:

All tests successful, 4 subtests skipped.
Files=121, Tests=5701, 241 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU).

Fortunately,  nmake does exit graciously and without errors!!

This will copy the modules to your perl\site\lib\ hierarchy, so they are available for inclusion in your scripts.

Ends with...

Writing C:\Perl\site\lib\auto\Bio\.packlist
Appending installation info to C:\Perl\lib/perllocal.pod