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Description:

CD-HIT is a very widely used program for clustering and comparing large sets of protein or nucleotide sequences. CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. CD-HIT-454 is a program to identify natural and artificial duplicates from pyrosequencing reads. The usage of other programs and scripts can be found in CD-HIT user's guide.

Homepage:

http://weizhong-lab.ucsd.edu/cd-hit/

License:

GPL-2

Versions

Metadata

Description

• CD-HIT is a very widely used program for clustering and comparing large sets of protein or nucleotide sequences. CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. CD-HIT-454 is a program to identify natural and artificial duplicates from pyrosequencing reads. The usage of other programs and scripts can be found in CD-HIT user's guide.

Maintainers

• Gentoo Biology Project (sci-biology@gentoo.org) - Type: project

Upstream

• Remote IDs:
  • google-code: cdhit
  • github: weizhongli/cdhit

<pkgmetadata>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<longdescription>
CD-HIT is a very widely used program for clustering and comparing large sets 
of protein or nucleotide sequences. CD-HIT is very fast and can handle 
extremely large databases. CD-HIT helps to significantly reduce the 
computational and manual efforts in many sequence analysis tasks and aids in 
understanding the data structure and correct the bias within a dataset.
The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
datasets and identifies the sequences in db2 that are similar to db1 above 
a threshold. CD-HIT-454 is a program to identify natural and artificial 
duplicates from pyrosequencing reads. The usage of other programs and 
scripts can be found in CD-HIT user's guide.
	</longdescription>
	<upstream>
		<remote-id type="google-code">cdhit</remote-id>
		<remote-id type="github">weizhongli/cdhit</remote-id>
	</upstream>
</pkgmetadata>

Lint Warnings

• [Warning] Ebuild 4.6.6-r1 uses IUSE flag 'openmp' which is not documented in metadata.xml. Add the flag to metadata.xml <use> section.
• [Warning] Missing md5-cache for version 4.6.6-r1. Run 'ebuild <ebuild_file> manifest' or 'egencache' to generate it.

USE Flags

Files

• cd-hit-4.6.6-fix-build-system.patch
• cd-hit-4.6.6-fix-perl-shebangs.patch

Manifest