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Port details
phred 0.020425.c biology on this many watch lists=0 search for ports that depend on this port
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Base calling and quality value assignment on DNA sequencing
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
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
  LI-COR 4000

Base calling accuracies tested for:
  ABI model 3100
  Beckman CEQ

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.html
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

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...

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


Configuration Options
     No options to configure

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Aug 2014 18:04:58
Original commit files touched by this commit  0.020425.c
Revision:365765
pi search for other commits by this committer
update ports:
	biology/phrab
	biology/phred
	biology/consed

Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.

PR:		191336
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
10 May 2014 18:07:52
Original commit files touched by this commit  0.020425.c
Revision:353593
antoine search for other commits by this committer
Replace maintainer's email address with one that seems to work

With hat:	portmgr
03 Jan 2014 15:46:52
Original commit files touched by this commit  0.020425.c
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  0.020425.c
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
19 Mar 2011 12:38:54
Original commit files touched by this commit  0.020425.c
miwi search for other commits by this committer
- Get Rid MD5 support
25 May 2008 23:05:10
Original commit files touched by this commit  0.020425.c
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:04:45
Original commit files touched by this commit  0.020425.c
edwin search for other commits by this committer
New port: biology/consed viewing and editing workbench for sequence
assembly

        Consed is a tool for viewing, editing, and finishing sequence
        assemblies.

        The port is constituted of 4 parts:
        biology/phred: base caller with quality evaluation
        biology/phrap: sequence assembler for shotgun sequencing
        biology/consed: workbench
        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.

PR:             ports/118548
Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>

Number of commits found: 7

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