./biology/glimmer, System for finding genes in microbial DNA

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Branch: CURRENT, Version: 2.13nb1, Package name: glimmer-2.13nb1, Maintainer: pkgsrc-users

Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.


Required to build:
[pkgtools/cwrappers]

Master sites:

Filesize: 77.986 KB

Version history: (Expand)

CVS history: (Expand)


   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2018-01-01 23:30:04 by Roland Illig | Files touched by this commit (537) 
Log message:
Sort PLIST files.

Unsorted entries in PLIST files have generated a pkglint warning for at
least 12 years. Somewhat more recently, pkglint has learned to sort
PLIST files automatically. Since pkglint 5.4.23, the sorting is only
done in obvious, simple cases. These have been applied by running:

  pkglint -Cnone,PLIST -Wnone,plist-sort -r -F
   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38) 
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2013-04-06 15:24:21 by Blue Rats | Files touched by this commit (21) 
Log message:
".for variable names should not contain uppercase letters"
   2012-09-16 19:20:17 by Aleksey Cheusov | Files touched by this commit (1) 
Log message:
CONFLICTS with generate-[0-9]*; ++pkgrevision
   2012-09-11 22:32:15 by Aleksej Saushev | Files touched by this commit (31) 
Log message:
"user-destdir" is default these days
   2009-06-14 19:34:35 by Joerg Sonnenberger | Files touched by this commit (21) 
Log message:
Remove @dirrm entries from PLISTs