phd2fastaConverter from output files of Phred/Consed to FASTA files
0.990622.fbiologyΣ=0 0.990622.fVersion of this port present on the latest quarterly branch.
DEPRECATED: Not staged. See http://lists.freebsd.org/pipermail/freebsd-ports-announce/2014-May/000080.html This port expired on: 2014-08-31 IGNORE: you must request the source code (phd2fasta-acd-dist.tar.Z) via e-mail, place it manually in /usr/local/PORTS-head/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.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
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
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.
CR: D196
Approved by: portmgr (bapt)
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>
