Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Trace data is read from chromatogram files in the SCF, ABI, and EST formats, even if they were compressed using gzip, bzip2, or UNIX compress. Quality values are written to FASTA format files or PHD files, which can be used by the Phrap sequence assembly program in order to increase the accuracy of the assembled sequence. Base calling and quality value accuracies tested for: ABI models 373, 377, and 3700 Molecular Dynamics MegaBACE LI-COR 4000 Base calling accuracies tested for: ABI model 3100 Beckman CEQ It contains also a data evaluation program called 'daev'. See DAEV.DOC for more information. You must obtain the tarball via e-mail to build. See the web site below. WWW: http://www.phrap.org/phredphrapconsed.html r> cgit logo index : freebsd-ports-gnome
FreeBSD GNOME current development ports (https://github.com/freebsd/freebsd-ports-gnome)
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* Correct squid user home directorycrees2012-10-281-1/+1
* - Upgrade to 0.10.27.kuriyama2012-10-271-0/+1
* Reserve username and groupname for devel/zookeeper{-devel}skreuzer2012-10-231-0/+1
* [devel/gearmand]:glarkin2012-10-051-0/+1
* Add net-mgmt/ipv6mon, a tool for monitoring IPv6 address usage on a localhrs2012-10-031-0/+1
* - Create gid and uid for tryton daemon and use them via USERS and GROUPS vari...wen2012-09-181-0/+1
* Update c-icap to 0.2.1mm2012-08-151-0/+1
* - use reserverd UID/GIDohauer2012-07-211-0/+1
* - Update to 1.3.9scheidell2012-07-081-0/+1
* add reserved UID/GID for polw (mail/postfix-policyd-weight)ohauer2012-06-071-0/+1
* Add UID and GID for net-mgmt/netmondcrees2012-05-311-0/+1
* preliminary version of update to 0.9.x; GUI, rc-scripts, tests,bf2012-05-291-0/+1
* - Add razorback USERS/GROUPS for upcoming security/razorback* port additionszi2012-05-211-0/+1
* Switch from old way to new way by using USERS.mezz2012-05-211-0/+1
* - Add USER/GROUP, missed from previous commitashish2012-05-161-0/+1
* Add Pandora FMS 4.0.1 - a Flexible Monitoring System.motoyuki2012-04-211-0/+1
* - Change /sbin/nologin to /usr/sbin/nologinsunpoet2012-04-181-1/+1
* Fix condor home directorycrees2012-04-181-1/+1
* Register username and groupname for condorcrees2012-04-131-0/+1
* - Add hadoop 1.0.0clement2012-03-271-0/+1
* Update SQLgrey to 1.8.0mm2012-02-141-0/+1
* Change type of pointers from int to uintptr_t for support 64 bit platforms.osa2012-02-021-0/+1
* Fix path for nologin(8).osa2012-02-021-3/+3
* - Functionality upgrade. Add in *.txt.sample files so that uninstall/pkg_del...scheidell2012-01-121-0/+1
* - Upgrade to 3.2.3.kuriyama2011-11-191-1/+1
* Reserve uid/gid 442 for Quassel IRCmakc2011-10-311-0/+1
* Spell /nonexistEnt correctly for freeswitch user, thus notcrees2011-10-291-1/+1
* Adding _neubot for Neubot's daemon.thierry2011-10-221-0/+1
* The KDE/FreeBSD team is pleased to announce KDE Software Compilationavilla2011-10-171-0/+1
* - Added user and group to prepare for new port devel/trac-bittenglarkin2011-10-141-0/+1
* Add the radns users/groupsbapt2011-09-281-0/+1
* Clarify UPDATING entry for maiad and update vscan user to new home dir.crees2011-09-051-1/+1
* - Add for openerp-serverbeech2011-09-021-0/+1
* Copy line from master.passwd for operator, not passwd.crees2011-08-241-1/+1
* Allow operator user to be used by a port.crees2011-08-241-0/+1
* - Add missing colon delimitersunpoet2011-08-221-16/+16
* - Change /sbin/nologin to /usr/sbin/nologinsunpoet2011-08-221-16/+16
* - Sync jenkins's home as ${JENKINS_HOME} in devel/jenkinslwhsu2011-08-201-1/+1
* Correct name in GECOS field and update shell to nologin.zi2011-08-171-1/+1
* mail/mixminion now uses USERScrees2011-08-151-0/+1
* net/gini now uses USERScrees2011-08-121-0/+1
* - Change zenoss user to have a valid shell, and add an UPDATING entry forpav2011-08-081-1/+1
* net/gatekeeper now uses USERS/GROUPScrees2011-07-261-0/+1
* Add users for net-mgmt/zenosscrees2011-07-221-0/+1
* Add missing entries for tr-ircdcrees2011-07-091-0/+1
* audio/ventrilo-server now uses USERS and GROUPScrees2011-07-081-0/+1
* - Fix a crash when an invalid log file is specified.hrs2011-07-021-0/+1
* Remove duplicate dbxml line.crees2011-06-291-1/+0
* Fix nobody user -- should be master.passwd stylecrees2011-06-151-1/+1
* - Correct GROUP when postfix OPTION is selected [1]crees2011-06-141-0/+1
* . Add entries for dbxml forgotten in databases/dbXML update.glewis2011-06-121-0/+1
* Add an user 'daapd' for audio/mt-daapdrene2011-06-071-0/+1
* Add entries for ports which are converted to the new USERS paradigm.rene2011-06-071-0/+7
* - add a current version of yate (3.3.2p1). This is not a repocopy offlo2011-05-221-0/+1
* - update tor-devel to 0.2.3.1-alphabf2011-05-081-1/+1
* adsuck is a DNS relay that returns NXdomain for hosts that match names in abapt2011-05-071-0/+1
* - Updated to 3.0.0.b30 [1]glarkin2011-05-041-0/+1
* - update to 2.8.3bapt2011-04-241-0/+1
* - Replace pkg-install and pkg-deinstall with USERS and GROUPS in Makefilelwhsu2011-04-231-1/+1
* Update webcamd to 0.1.24.kwm2011-04-211-0/+1
* - Add _tcpproxy for new port net/tcpproxydhn2011-04-031-0/+1
* - rename hobbit to xymondinoex2011-04-021-1/+1
* - Pass -Dbsd_with_getifaddrs to CFLAGS in order to get a correct networkehaupt2011-03-291-0/+1
* Reserve IDs for multimedia/vdr and related ports.nox2011-03-271-0/+1
* Register uid and gid for net/get_iplayerbf2011-03-091-0/+1
* - Register UID and GID for devel/jenkinslwhsu2011-03-071-0/+1
* - Register uid and gid for net/crtmpserversylvio2011-02-281-0/+1
* - Register uid and gid for net-mgmt/icingachinsan2011-02-241-0/+1
* - Register uid and gid for net/erlyvideomiwi2011-02-021-0/+1
* - fix format of my last commit for UID 587ohauer2011-01-061-1/+1
* - register UID/GID 587 for assp user (port mail/assp)ohauer2011-01-061-0/+1
* - Move torrus user to next unoccupied slotpav2010-12-241-1/+1
* - Upgrade to USERS/GROUPSpav2010-12-231-0/+1
* - register UID/GID 542 for _flowd user (port net-mgmt/flowd)ohauer2010-12-211-0/+1
* Add the port of minidlna -- the DLNA-speaking service.mi2010-12-141-0/+1
* Dont declare ${sancp_flags} in command_args.wxs2010-12-131-0/+1
* - add radmind with uid/gid 506 for port sysutils/radmindohauer2010-11-281-0/+1
* . Add a port of the 2.x series of Dovecot:glewis2010-11-271-0/+1
* * Sets up a uhub UID and GID for the daemon to run as.stefan2010-11-111-0/+1
* Add "asterisk" user/group and "dahdi" group.fjoe2010-11-071-0/+1
* Add _tss and _pkcs11 to reserve for security/trousers andnork2010-11-071-0/+2
* Finally upgrade amanda-{server,client} to 3.2.0. Old 2.6.x waskuriyama2010-11-011-0/+1
* - add RC scriptswills2010-10-111-0/+1
* Archiveopteryx is an Internet mail server, optimised to supportashish2010-10-031-0/+1
* BackupPC is a high-performance, enterprise-grade system for backing up Linux,pgollucci2010-09-231-0/+1
* - Convert to USERS/GROUPSpgollucci2010-09-221-0/+1
* tWMS is a tiny WMS server written in Python and using tiles as aamdmi32010-09-081-0/+1
* Use the USERS/GROUPS mechanismlth2010-08-121-0/+1
* - Add user/group shellinabox with uid/gid 139jadawin2010-07-051-0/+1
* Add 'saned' user/group the Right Way.stefan2010-06-281-0/+1
* Fix missing fields in previous commitjpaetzel2010-06-131-1/+1
* - Add activemq for new port net/activemqwen2010-06-121-0/+1
* Add net/freeswitch-core, part of a revamp to the freeswitch portsjpaetzel2010-06-121-0/+1
* - fix Text for meta1dinoex2010-06-041-1/+1
* - Update to 0.7.3pav2010-05-141-0/+1
* Change the home directory of p4admin to /nonexistent because it is not needed.rene2010-05-101-1/+1
* - Added user and group for Drizzle database serverglarkin2010-04-291-0/+1
* - Reserve kumofs uid/gid.kuriyama2010-04-261-0/+1
* - Update to v1.2.6abrix2010-04-241-1/+1
* Minbif aims to use the libpurple library from the Pidgin projectbeat2010-04-151-0/+1
* - Add user and group mfs for MooseFS portwen2010-04-071-0/+1
* - Fix malformed lines, per new portlint(1) checkpav2010-04-061-4/+4
* - reserver GID/UID 924 for upcomming mail/postpalsitetcu2010-03-131-0/+1
* Massive cleanup of the Munin ports:des2010-02-251-0/+1
* - Add user and group for audio/liquidsoapwen2010-02-011-0/+1
* - Update Wolfpack Empire to 4.3.23johans2009-12-281-0/+1
* - Reserve UID/GID 137 for audio/musicpdpav2009-12-071-0/+1
* - Prepare for add new port databases/mongodbwen2009-11-191-0/+1
* - Add 444 for callweaverpav2009-09-181-0/+1
* - Update to 0.8.5beat2009-09-181-0/+1
* - Add UID/GID:211 for devel/py-gitosisnivit2009-09-161-0/+1
* - Fix typo in directory name for undernet user.flz2009-09-111-2/+2
* Add haldaemon with UID/GID 560.flz2009-09-071-0/+1
* Add UID and GID forgotten while adding net-mgmt/noc.bsam2009-08-181-0/+1
* - unbound does not use `unbound' group anymore, but `daemmon' insteadsem2009-08-171-1/+1
* Remove entries for security/trans-proxy-tor and security/dns-proxy-torerwin2009-08-161-2/+0
* Add prosody entries to UIDs & GIDs.vanilla2009-08-051-0/+1
* Register user/group "redis" for the port "databases/redis".skv2009-07-281-0/+1
* - Unify path to nologin as /usr/sbin/nologin. This has been done at leastwxs2009-07-251-8/+8
* - Add fossy user/group for devel/fossology.alepulver2009-07-241-0/+1
* -Add transmission.mezz2009-06-201-1/+2
* - Add GID and UID for emulators/virtualbox.beat2009-06-181-0/+1
* - Add couchdb user and group.wxs2009-06-171-0/+1
* - Register net-mgmt/nefurafan2009-04-071-0/+1
* - Register uid and gid for mail/prayerrafan2009-03-171-0/+1
* Reflect the change of UID/GID of ejabberd.delphij2009-03-161-1/+1
* - Updated to 0.21glarkin2009-03-111-1/+1
* Rework on rc script for www/httptunnel.rafan2009-01-301-0/+1
* Register a fixed UID/GID for the user 'dhcpd' and use that instead of astefan2009-01-121-0/+1
* - Add UID and GID entries for net/rabbitmq.wxs2008-10-291-0/+1
* - Fixed logcheck script silent failure in previous commitglarkin2008-09-111-1/+1
* - Fixed left-over directory problemglarkin2008-09-091-0/+1
* - Update pgbouncer to 1.2.3mm2008-08-121-0/+1
* Reserve numbers for databases/frontbase user.edwin2008-06-131-0/+1
* Switch UIDs to master.passwd compatible format.flz2008-05-201-142/+142
* Style fix, $FreeBSD$ line is a comment, so add a leading '#'.flz2008-05-201-1/+1
* Reserve UID and GID for irc/bitlbee.brix2008-05-201-0/+1
* - Add entries for irc/undernet-ircubeech2008-05-011-0/+1
* - Reserve GID/UID 59 for dns/unboundsem2008-04-291-0/+1
* Reserve 814 for sysutils/puppet*pav2008-04-111-0/+1
* - Add GID and UID for www/openacs and www/openacs-dotlrnmm2008-04-031-0/+2
* - Add GID and UID for net/freeradius2mm2008-04-021-0/+1
* * Don't need p5-Digest-MD5; p5-libwww dependency takes care of that.koitsu2008-03-101-1/+1
* - Register UID for net/phpldapadmin, net/phpldapadmin098rafan2008-03-091-0/+1
* - Add GID and UID for net-im/openfiremiwi2008-03-081-0/+1
* Remove IGNORE; add UID 141 to ports/UIDs, and remove unnecessary Time::HiReskoitsu2008-02-191-0/+1
* - Sort UIDsmiwi2008-02-171-2/+2
* - add hobbit with id 280dinoex2008-01-281-0/+1
* - Reserve UID/GID 240 and 241 for aprsddb2008-01-241-0/+2
* Changes:miwi2008-01-211-0/+1
* Add 913 for _relayd.kuriyama2008-01-211-0/+1
* Inconsistent format of lines in /usr/ports/UIDsedwin2008-01-191-4/+4
* - Reserve uid/gid for net/iodine 0.4.1_1rafan2008-01-111-0/+1
* Unify nologin path to /usr/sbin/nologinedwin2007-09-301-75/+75
* Add _sj3 for japanese/sj3 with UID 912edwin2007-09-091-1/+2
* Add 911 for iserv (See PR ports/114017)edwin2007-09-071-0/+1
* Reserve a user and group ID for the stunnel daemon.roam2007-08-281-0/+1
* - Update to 1.28beech2007-06-281-0/+1
* - Move zabbix from UID 112 to 122 to avoid conflict with dccsat2007-06-221-0/+1
* - add MeTA1dinoex2007-06-101-5/+5
* - Update to 0.9.8miwi2007-05-301-0/+1
* Reserve a UID for pulse and a GID for pulse and pulse-access. These are neededmarcus2007-04-301-0/+1
* - Sorted otrs correctmiwi2007-04-211-1/+1
* Register UID and UID for mail/nullmailer.clive2007-04-211-1/+2
* - Add UID/GID for devel/otrsmiwi2007-04-111-0/+1
* - Use static gid/uid.stas2007-04-111-0/+1
* (second attempt)naddy2007-04-101-1/+1
* reserve _ntp UID/GID for OpenNTPDnaddy2007-04-101-0/+1
* - Give irc/hybserv a unique UID/GIDlaszlof2007-03-311-0/+1
* Register UID and GID for net-mgmt/netdisco.shaun2007-03-281-0/+1
* Correct a copy-paste problem when allocating the polkit UID, and use a uniquemarcus2007-03-241-0/+1
* Reserve UID and GID for net-mgmt/nav.des2007-03-131-0/+1
* Add GID and UID for OpenBSD spamd (mail/spamd).delphij2007-03-091-0/+1
* - change smx entries to "/usr/sbin/nologin"dinoex2007-02-171-5/+5
* - add smmspdinoex2007-02-171-0/+1
* - Reserve UID/GID 312 for sphinxpav2007-01-311-0/+1
* - Reserve UID/GID 181 for nagiospav2007-01-281-0/+1
* - Register UID/GID for pdns_recursorpav2007-01-191-0/+1
* - Add user/group for sysutils/fcronrafan2007-01-171-0/+1
* Add user and group mythtv (119).grog2007-01-141-0/+1
* Add missing colon to the cups entry.shaun2006-12-281-1/+1
* - register cupsdinoex2006-12-181-0/+1
* - Reserve UID/GID 143 for mail/dovecotpav2006-12-011-0/+1
* - add wildfire to GIDs and UIDsalexbl2006-11-161-0/+1
* Register mail/fetchmail's UID and GID.barner2006-11-151-0/+1
* - Reserve UID and GID 561 for distccahze2006-11-121-0/+1
* Oops, restore dkfilter, still needed for dkfilter portache2006-11-091-0/+1
* Remove bogomilter and dkfilterache2006-11-091-2/+0
* - Add _xsi user and group for sysutils/xsi.alepulver2006-11-061-0/+1
* - Add entry for net-mgmt/bigsisterrafan2006-11-041-0/+1
* - Add hacluster user.alepulver2006-11-021-0/+1
* Reserve uid:gid 559 for the tacacs user for net/tac_plus4.marcus2006-10-311-0/+1
* This file lists entries in passwd(5) format; fix those three that didn't agree.ru2006-09-041-3/+3
* - Register UID/GID 128 for vserverpav2006-08-291-0/+1
* - Reserve UID/GID 118 for irc/ircproxypav2006-08-291-0/+1
* Add ID for Tiarra IRC Proxy.ume2006-07-291-0/+1
* - rc.d scripts are changed to show error messages when some errorrafan2006-07-291-0/+1
* Add user/group for mail/dkimproxy, which is added two days ago.rafan2006-07-291-0/+1
* Reserve uid/gid for net/smokepinglth2006-07-261-0/+1
* Fix home directory for "firebird" user:skv2006-07-251-1/+1
* Reserve uid/gid for Openlink Virtuoso Universal Server.fjoe2006-07-251-0/+1
* Add entry for trans-proxy-tor.miwi2006-07-221-0/+1
* Add entry for dns-proxy-tor.miwi2006-07-221-0/+1
* Add $FreeBSD tag.krion2006-07-221-0/+1