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cd-hit-auxtools Bug fix in variable length input when write out R1 reads Jul 12, 2016
doc doc/cd-hit-otu-miseq-Figure-1.png Jun 19, 2017
psi-cd-hit psi-cd-hit/psi-cd-hit-local.pl minor fix for user Jul 11, 2018
usecases usecases/Miseq-16S/README path fix Dec 8, 2017
ChangeLog Rebase and add minor changes. Mar 21, 2013
FET.pl included 3 scripts needed by cdhit-web-server May 23, 2017
Makefile Update Makefile, make openmp as default May 13, 2015
README README update Jun 21, 2017
cd-hit-2d-para.pl Rebase and add minor changes. Mar 21, 2013
cd-hit-clstr_2_blm8.pl cd-hit-clstr_2_blm8.pl copied from NGS-tools directory Oct 19, 2017
cd-hit-div.pl Rebase and add minor changes. Mar 21, 2013
cd-hit-para.pl Rebase and add minor changes. Mar 21, 2013
cdhit-2d.c++ Rebase and add minor changes. Mar 21, 2013
cdhit-454.c++ Rebase and add minor changes. Mar 21, 2013
cdhit-common.c++ test to add PE mode to cd-hit-est-2d Apr 27, 2017
cdhit-common.h cdhit-utility.c++ Apr 28, 2017
cdhit-div.c++ Rebase and add minor changes. Mar 21, 2013
cdhit-est-2d.c++ test to add PE mode to cd-hit-est-2d Apr 27, 2017
cdhit-est.c++ cdhit-common.c++ Oct 27, 2016
cdhit-utility.c++ cdhit-utility.c++ May 1, 2017
cdhit-utility.h Rebase and add minor changes. Mar 21, 2013
cdhit.c++ Rebase and add minor changes. Mar 21, 2013
clstr2tree.pl Rebase and add minor changes. Mar 21, 2013
clstr2txt.pl Rebase and add minor changes. Mar 21, 2013
clstr2xml.pl Rebase and add minor changes. Mar 21, 2013
clstr_cut.pl Rebase and add minor changes. Mar 21, 2013
clstr_list.pl included 3 scripts needed by cdhit-web-server May 23, 2017
clstr_list_sort.pl included 3 scripts needed by cdhit-web-server May 23, 2017
clstr_merge.pl Rebase and add minor changes. Mar 21, 2013
clstr_merge_noorder.pl Rebase and add minor changes. Mar 21, 2013
clstr_quality_eval.pl Rebase and add minor changes. Mar 21, 2013
clstr_quality_eval_by_link.pl Rebase and add minor changes. Mar 21, 2013
clstr_reduce.pl Rebase and add minor changes. Mar 21, 2013
clstr_renumber.pl Rebase and add minor changes. Mar 21, 2013
clstr_rep.pl Rebase and add minor changes. Mar 21, 2013
clstr_reps_faa_rev.pl Rebase and add minor changes. Mar 21, 2013
clstr_rev.pl Rebase and add minor changes. Mar 21, 2013
clstr_select.pl Rebase and add minor changes. Mar 21, 2013
clstr_select_rep.pl Rebase and add minor changes. Mar 21, 2013
clstr_size_histogram.pl Rebase and add minor changes. Mar 21, 2013
clstr_size_stat.pl Rebase and add minor changes. Mar 21, 2013
clstr_sort_by.pl Rebase and add minor changes. Mar 21, 2013
clstr_sort_prot_by.pl Rebase and add minor changes. Mar 21, 2013
clstr_sql_tbl.pl Rebase and add minor changes. Mar 21, 2013
clstr_sql_tbl_sort.pl Rebase and add minor changes. Mar 21, 2013
license.txt Rebase and add minor changes. Mar 21, 2013
make_multi_seq.pl Rebase and add minor changes. Mar 21, 2013
plot_2d.pl Rebase and add minor changes. Mar 21, 2013
plot_len1.pl Rebase and add minor changes. Mar 21, 2013

README

For cd-hit

How to compile?
  1. Compile with multi-threading support (default): make
  2. Compile without multi-threading support (if you are on very old systems): make openmp=no


For cd-hit-auxtools
  cd cd-hit-auxtools
  make


For psi-cd-hit
  please download legacy BLAST (not BLAST+) and install the executables in your $PATH


For more information, please visit http://cd-hit.org

Most up-to-date documents are available at https://github.com/weizhongli/cdhit/wiki

cd-hit is also available as web server, visit http://cd-hit.org for web server address.