- phrap Phrap is a program for assembling shotgun DNA sequence data
1.090518 biology =0
- IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/local/PORTS-head/distfiles/phrap, and then try it again
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 07:03:43
License: not specified in port
Phrap is a program for assembling shotgun DNA sequence data.
Among other features, it allows use of the entire read and not just the
trimmed high quality part, it uses a combination of user-supplied and
internally computed data quality information to improve assembly accuracy
in the presence of repeats, it constructs the contig sequence as a mosaic
of the highest quality read segments rather than a consensus, it provides
extensive assembly information to assist in trouble-shooting assembly
problems, and it handles large datasets.
This package also contains Swat and Cross_match.
Swat is a program for searching one or more DNA or protein query sequences
against a sequence database, using (an efficient implementation of) the
Cross_Match is a general-purpose utility based on Swat for comparing any
two sets of DNA sequences, and it can be used to:
* produce vector-masked versions of a set of reads
* compare a set of cDNA sequences to a set of cosmids
* compare contigs found by two altanative assembly procedures to each other
* compare phrap contigs to the final edited cosmid sequence.
WWW: http://www.phrap.org/phredphrapconsed.htmlSVNWeb : Homepage : PortsMon
To install the port:
cd /usr/ports/biology/phrap/ && make install clean
A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted
SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665
SIZE (phrap/distrib.tar.gz) = 333159
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
There is no master site for this port.
Number of commits found: 8
|Commit History - (may be incomplete: see SVNWeb link above for full details)
|16 Oct 2014 08:55:30
- Fix various distinfo errors
- Remove unused USE_* knobs
- Fix typos in USE_* knobs
- Remove empty lines after .include <bsd.port.mk>
Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D911
|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 07:03:23
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: 8
13 vulnerabilities affecting 49 ports have been reported in the past 14 days
* - modified, not new