phrap 0.990329 biology =0

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: 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
Port Added: 24 May 2008 08:03:43

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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

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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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

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Configuration Options

     No options to configure

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Master Sites:

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/phrap/

Teach the building cluster that these ports are not to be build

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>

5 vulnerabilities affecting 16 ports have been reported in the past 14 days

^* - modified, not new

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