2dd0 FreshPorts -- biology/phrap
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Port details
phrap 0.990329 biology on this many watch lists=0 search for ports that depend on this port
Ignore IGNORE: you must request the source code \(distrib.tar.Z\) via e-mail, place it manually in /usr/ports/distfiles/phrap, and then try it again
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Phrap is a program for assembling shotgun DNA sequence data
Maintained by: mzaki@biol.s.u-tokyo.ac.jp search for ports maintained by this maintainer
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
Smith-Waterman-Gotoh algorithm.
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.html
SVNWeb : Main Web Site : Distfiles Availability : PortsMonThere are no ports dependent upon this port

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


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/phrap/

Number of commits found: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Mar 2011 12:38:54
Original commit files touched by this commit  0.990329
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  0.990329
edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
24 May 2008 07:03:23
Original commit files touched by this commit  0.990329
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: 3

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