<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <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>