05-05-2011
Does my provider limit my internet access or somesites access?
Hi
Good Day, i would like to ask for further info about my problems experiencing this evening. Im a PPP0 connection in the internet using 3G located in asia pacific region.i had this problem this evening in my INTERNET connections that there are some sites i can't open example ( Gizmodo.com, launchpad.net) but other site was fine and ok. I try the error site in my company networks and guess what its ok. When i use my seamonkey browser configure to browse encryption using tor networks. i can open the following sites but i dont want to use mostly the encrypted connection on my seamonkey cause the speed limitation. its takes time to load the sites.
Thanks for any reply.
---------- Post updated at 06:27 AM ---------- Previous update was at 05:14 AM ----------
i think maybe the problem is in my network and network provider. They block those site and many much more. Only two i list cause thats the two i always revisited. I try my 3g connection with my linux mint bootable USB and the same problem can't reach some of the sites. Am i correct any additional idea will help.
---------- Post updated at 06:44 AM ---------- Previous update was at 06:27 AM ----------
Just this morning the internet sites having problem on my networks is now restore or accesible..i guess my provider have some configuration task list this past evening.
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LEARN ABOUT DEBIAN
bio::popgen::utilities
Bio::PopGen::Utilities(3pm) User Contributed Perl Documentation Bio::PopGen::Utilities(3pm)
NAME
Bio::PopGen::Utilities - Utilities for working with PopGen data and objects
SYNOPSIS
use Bio::PopGen::Utilities;
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-file => 't/data/t7.aln',
-format => 'clustalw');
my $aln = $in->next_aln;
# get a population, each sequence is an individual and
# for the default case, every site which is not monomorphic
# is a 'marker'. Each individual will have a 'genotype' for the
# site which will be the specific base in the alignment at that
# site
my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln);
# get the synonymous sites from the alignemt only as the 'genotypes'
# for the population
my $synpop = Bio::PopGen::Utilities->aln_to_population(-site_model => 'cod',
-alignment => $aln);
DESCRIPTION
This object provides some convience function to turn sequence alignments into usable objects for the Population genetics modules
(Bio::PopGen).
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
aln_to_population
Title : aln_to_population
Usage : my $pop = Bio::PopGen::Utilities->aln_to_population($aln);
Function: Turn and alignment into a set of L<Bio::PopGen::Individual>
objects grouped in a L<Bio::PopGen::Population> object
Sites are treated as 'Markers' in the Bioperl PopGen object
model in the sense that a site is a unique location for which
an individual will have a genotype (a set of alleles).
In this implementation we are assuming that each individual
has a single entry in the alignment file.
Specify a site model as one of those listed
'all' -- every base in the alignment is considered a site
'cod' -- codons
The option -site_model
for All sites : 'all'
Codon sites : 'cod' or 'codon'
To see all sites, including those which are fixed in the population
add -include_monomorphic => 1
to the arguments
Returns :
Args : -include_monomorphic => 1 to specify all sites,
even those which are monomorphic
in the population
(useful for HKA test mostly)
[default is false]
-phase => specify a phase for the data, this is only
used if the site_mode is codon
[default is 0]
-site_model => one-of 'all', 'codon'
to specify a site model for the data extraction
from the alignment
[default is all]
-alignment => provide a L<Bio::SimpleAlign> object [required]
perl v5.14.2 2012-03-02 Bio::PopGen::Utilities(3pm)