phd2fasta 0.990622.f biology =0

IGNORE: you must request the source code \(phd2fasta-acd-dist.tar.Z\) via e-mail, place it manually in /usr/ports/distfiles, 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.
A converter from output files of Phred/Consed to FASTA files
Maintained by: mzaki@biol.s.u-tokyo.ac.jp
Port Added: 24 May 2008 07:02:33
License: not specified in port

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Phred and consed write sequence and quality value information in
'phd' output files. A phd file contains information in a header,
the called bases, the base quality values, and the base call trace
locations.  Phd2fasta reads phd files and writes sequence and quality
value FASTA files, which phrap and cross_match need as input.
(Consed needs phd files in order to obtain the base call locations.)

WWW: http://www.phrap.org/phredphrapconsed.html

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMonThere are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/phd2fasta/ && 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/

- Get Rid MD5 support

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>

14 vulnerabilities affecting 33 ports have been reported in the past 14 days

^* - modified, not new

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