BSD Ports

biology/fastdnaml 1.2.2_2 FreeBSD

Faster DNAML, makes phylogenetic trees using maximum likelihood

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
GPLv2+
Categories
biology
Package size
54.3 KiB, 141.0 KiB installed

Description

fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program.

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

In the other systems

The newest version among them is 1.2.2, as upstream numbers it.

SystemPortVersionVulnerabilitiesStatusMaintainerLast update
FreeBSDbiology/fastdnaml1.2.2_2 newestnone known-[email protected]-
DragonFlybiology/fastdnaml1.2.2_2 newestnone known-[email protected]-
HardenedBSDbiology/fastdnaml1.2.2_2 newestno data-[email protected]-
GhostBSDbiology/fastdnaml1.2.2_2 newestno data-[email protected]-

Install

Binary package:

pkg install fastdnaml

From the ports tree:

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

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

RUN_DEPENDS=	fastdnaml>0:biology/fastdnaml

Packages

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

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest1.2.2_21.2.2_21.2.2_21.2.2_21.2.2_2
FreeBSD:14:quarterly1.2.2_21.2.2_2n/a1.2.2_21.2.2_2
FreeBSD:15:latest1.2.2_21.2.2_2n/a1.2.2_21.2.2_2
FreeBSD:15:quarterly1.2.2_21.2.2_2n/an/an/a
FreeBSD:16:latest1.2.2_21.2.2_2n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/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_fastdnaml

OptionDefaultDescription
DOCSoffBuild and/or install documentation
Service scripts
none

Message after installing

===>   NOTICE:

The fastdnaml port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 34
  • bin/fastDNAml
  • bin/fastdnaml/ae2dnaml
  • bin/fastdnaml/bootstrap
  • bin/fastdnaml/categories
  • bin/fastdnaml/categories_file
  • bin/fastdnaml/checkpoint_summary
  • bin/fastdnaml/clean_checkpoints
  • bin/fastdnaml/clean_jumbles
  • bin/fastdnaml/dnaml_progress
  • bin/fastdnaml/fastDNAml_boot
  • bin/fastdnaml/fastDNAml_loop
  • bin/fastdnaml/frequencies
  • bin/fastdnaml/global
  • bin/fastdnaml/iterate_rates
  • bin/fastdnaml/jumble
  • bin/fastdnaml/min_info
  • bin/fastdnaml/n_categories
  • bin/fastdnaml/n_files
  • bin/fastdnaml/out.PID
  • bin/fastdnaml/outgroup
  • bin/fastdnaml/printdata
  • bin/fastdnaml/quickadd
  • bin/fastdnaml/restart
  • bin/fastdnaml/scores
  • bin/fastdnaml/transition
  • bin/fastdnaml/treefile
  • bin/fastdnaml/treefile2prolog
  • bin/fastdnaml/trees2NEXUS
  • bin/fastdnaml/trees2prolog
  • bin/fastdnaml/userlengths
  • bin/fastdnaml/usertree
  • bin/fastdnaml/usertrees
  • bin/fastdnaml/weights
  • bin/fastdnaml/weights_categories
distinfo 1
FileSizeSHA256
fastDNAml_1.2.2.tar.gz7000534690ec9a8e2fe1d86bea4a7cb10f7bc47e5e4c30719e1c9451210df4f160180
Master sites 1
  • http://www.life.illinois.edu/gary/programs/fastDNAml/

Commit history 0

No commits in the history this site was built from.