- phred Base calling and quality value assignment on DNA sequencing
0.020425.c biology =0
- RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Port Added: 24 May 2008 07:05:09
License: not specified in port
Phred reads DNA sequencer trace data, calls bases, assigns quality values
to the bases, and writes the base calls and quality values to output files.
Trace data is read from chromatogram files in the SCF, ABI, and EST formats,
even if they were compressed using gzip, bzip2, or UNIX compress.
Quality values are written to FASTA format files or PHD files, which can be
used by the Phrap sequence assembly program in order to increase the accuracy
of the assembled sequence.
Base calling and quality value accuracies tested for:
ABI models 373, 377, and 3700
Molecular Dynamics MegaBACE
Base calling accuracies tested for:
ABI model 3100
It contains also a data evaluation program called 'daev'.
See DAEV.DOC for more information.
You must obtain the tarball via e-mail to build. See the web site below.
WWW: http://www.phrap.org/phredphrapconsed.htmlSVNWeb : Homepage : PortsMon
To install the port:
cd /usr/ports/biology/phred/ && make install clean
A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted
This port is required by:for Run
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
No options to configure
Number of commits found: 7
|Commit History - (may be incomplete: see SVNWeb link above for full details)
|23 Aug 2014 18:04:58
Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.
Submitted by: email@example.com (maintainer)
|10 May 2014 18:07:52
Replace maintainer's email address with one that seems to work
With hat: portmgr
|03 Jan 2014 15:46:52
Convert biology to MDOCS and MEXAMPLES
|20 Sep 2013 15:55:44
Add NO_STAGE all over the place in preparation for the staging support (cat:
|19 Mar 2011 12:38:54
- Get Rid MD5 support
|25 May 2008 23:05:10
Teach the building cluster that these ports are not to be build
|24 May 2008 07:04:45
New port: biology/consed viewing and editing workbench for sequence
Consed is a tool for viewing, editing, and finishing sequence
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
Submitted by: Motomichi Matsuzaki <firstname.lastname@example.org>
Number of commits found: 7
7 vulnerabilities affecting 19 ports have been reported in the past 14 days
* - modified, not new