biology/fasta3 36.3.8_1 FreeBSD

Collection of programs for searching DNA and protein databases

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
License: Fasta
Categories: biology
Package size: 724.6 KiB, 5414.4 KiB installed

Description

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta.

FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in Molecular Biology 132:185-219.

The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

In the other systems

System

Port

Version

FreeBSD

biology/fasta3

36.3.8_1

DragonFly

biology/fasta3

36.3.8_1

HardenedBSD

biology/fasta3

36.3.8_1

GhostBSD

biology/fasta3

36.3.8_1

Install

Binary package:

pkg install fasta3

From the ports tree:

cd /usr/ports/biology/fasta3/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	fasta3>0:biology/fasta3

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

36.3.8_1

36.3.8

36.3.8_1

FreeBSD:14:quarterly

36.3.8_1

n/a

36.3.8_1

FreeBSD:15:latest

36.3.8_1

n/a

36.3.8_1

FreeBSD:15:quarterly

36.3.8_1

n/a

FreeBSD:16:latest

36.3.8_1

n/a

FreeBSD:16:quarterly

n/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

No port depends on this one.

Configuration

Options name: biology_fasta3

Option

Default

Description

DOCS

off

Build and/or install documentation

EXAMPLES

off

Build and/or install examples

Service scripts: none

Message after installing

The FASTA3 package has been successfully installed.

 A sample configuration file has been installed to
 /usr/local/etc
 as "fastlibs.sample". This may be renamed to "fastlibs" and edited
 to suit the requirements of a particular site.

 In order to use the FASTA3 programs, a user must set the environment
 variable FASTLIBS to contain the full path of the FASTA3 configuration
 file, e.g.:

 set FASTLIBS to: "/usr/local/etc/fastlibs"

Files

Manual pages 21

fasta36(1)
fastf3(1)
fastf35(1)
fastm35(1)
fasts3(1)
fasts35(1)
fastx35(1)
fasty35(1)
ggsearch35(1)
lalign35(1)
map_db(1)
prfx35(1)
prss3(1)
prss35(1)
ps_lav(1)
ssearch35(1)
tfasta35(1)
tfastf35(1)
tfasts35(1)
tfastx35(1)
tfasty35(1)

pkg-plist 125

bin/fasta
bin/fastf
bin/fastm
bin/fasts
bin/fastx
bin/fasty
bin/ggsearch
bin/glsearch
bin/lalign
bin/map_db
bin/ssearch
bin/tfastf
bin/tfastm
bin/tfasts
bin/tfastx
bin/tfasty
etc/fastlibs.sample
share/man/man1/fasta36.1.gz
share/man/man1/fastf3.1.gz
share/man/man1/fastf35.1.gz
share/man/man1/fastm35.1.gz
share/man/man1/fasts3.1.gz
share/man/man1/fasts35.1.gz
share/man/man1/fastx35.1.gz
share/man/man1/fasty35.1.gz
share/man/man1/ggsearch35.1.gz
share/man/man1/lalign35.1.gz
share/man/man1/map_db.1.gz
share/man/man1/prfx35.1.gz
share/man/man1/prss3.1.gz
share/man/man1/prss35.1.gz
share/man/man1/ps_lav.1.gz
share/man/man1/ssearch35.1.gz
share/man/man1/tfasta35.1.gz
share/man/man1/tfastf35.1.gz
share/man/man1/tfasts35.1.gz
share/man/man1/tfastx35.1.gz
share/man/man1/tfasty35.1.gz
share/doc/fasta3/COPYRIGHT
share/doc/fasta3/FASTA_LIST
share/doc/fasta3/README
share/doc/fasta3/README.versions
share/doc/fasta3/changes_v34.html
share/doc/fasta3/changes_v35.html
share/doc/fasta3/changes_v36.html
share/doc/fasta3/fasta.defaults
share/doc/fasta3/fasta.options
share/doc/fasta3/fasta_func.doc
share/doc/fasta3/fasta_versions.html
share/doc/fasta3/readme.v30
share/doc/fasta3/readme.v30t6
share/doc/fasta3/readme.v30t7
share/doc/fasta3/readme.v31t0
share/doc/fasta3/readme.v31t1
share/doc/fasta3/readme.v32t0
share/doc/fasta3/readme.v33t0
share/doc/fasta3/readme.v34t0
share/doc/fasta3/readme.v35
share/doc/fasta3/readme.v36
share/doc/fasta3/readme.w32
share/examples/fasta3/bovgh.seq
share/examples/fasta3/bovprl.seq
share/examples/fasta3/dyr_human.aa
share/examples/fasta3/egmsmg.aa
share/examples/fasta3/gst.seq
share/examples/fasta3/gstt1_drome.aa
share/examples/fasta3/gtm1_human.aa
share/examples/fasta3/gtt1_drome.aa
share/examples/fasta3/h10_human.aa
share/examples/fasta3/hahu.aa
share/examples/fasta3/hsgstm1b.seq
share/examples/fasta3/humgstd.seq
share/examples/fasta3/lcbo.aa
share/examples/fasta3/m1r.aa
share/examples/fasta3/m2.aa
share/examples/fasta3/mchu.aa
share/examples/fasta3/mgstm1.aa
share/examples/fasta3/mgstm1.lc
share/examples/fasta3/mgstm1.seq
share/examples/fasta3/mgstm1_genclone.seq
share/examples/fasta3/mgtt2_x.seq
share/examples/fasta3/ms1.aa
share/examples/fasta3/mu.lib
share/examples/fasta3/musplfm.aa
share/examples/fasta3/mwkw.aa
share/examples/fasta3/mwrtc1.aa
share/examples/fasta3/myosin_bp.aa
share/examples/fasta3/n0.aa
share/examples/fasta3/n1.aa
share/examples/fasta3/n2.aa
share/examples/fasta3/n2_fs.lib
share/examples/fasta3/n2s.aa
share/examples/fasta3/n2t.aa
share/examples/fasta3/n_fs.lib
share/examples/fasta3/ngt.aa
share/examples/fasta3/ngts.aa
share/examples/fasta3/oohu.aa
share/examples/fasta3/prio_atepa.aa
share/examples/fasta3/prot_test.lib
share/examples/fasta3/qrhuld.aa

The first 100 are listed.

distinfo 1

File

Size

SHA256

fasta3/2014-01-29/fasta-36.3.8.tar.gz

1.211304e+06

e235458afd16591bbcd5b89b639497e20346841091440a2445593318510a2262

Master sites 1

http://faculty.virginia.edu/wrpearson/fasta/fasta36/

Commit history 0

No commits in the history this site was built from.