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| .. | | 03-May-2022 | - |
| cd-hit-auxtools/ | H | 28-Feb-2019 | - | 3,840 | 3,317 |
| doc/ | H | 03-May-2022 | - | 2,739 | 2,213 |
| psi-cd-hit/ | H | 28-Feb-2019 | - | 3,805 | 2,999 |
| usecases/ | H | 28-Feb-2019 | - | 4,342 | 3,397 |
| ChangeLog | H A D | 28-Feb-2019 | 2.3 KiB | 83 | 61 |
| FET.pl | H A D | 03-May-2022 | 3.1 KiB | 110 | 69 |
| Makefile | H A D | 03-May-2022 | 2.5 KiB | 110 | 65 |
| README | H A D | 28-Feb-2019 | 1.4 KiB | 43 | 29 |
| cd-hit-2d-para.pl | H A D | 03-May-2022 | 12.3 KiB | 484 | 399 |
| cd-hit-clstr_2_blm8.pl | H A D | 03-May-2022 | 2.1 KiB | 59 | 40 |
| cd-hit-div.pl | H A D | 03-May-2022 | 883 | 50 | 40 |
| cd-hit-para.pl | H A D | 03-May-2022 | 11.6 KiB | 455 | 377 |
| cdhit-2d.c++ | H A D | 28-Feb-2019 | 2.4 KiB | 79 | 36 |
| cdhit-454.c++ | H A D | 28-Feb-2019 | 3.1 KiB | 109 | 55 |
| cdhit-common.c++ | H A D | 28-Feb-2019 | 141.8 KiB | 4,409 | 3,778 |
| cdhit-common.h | H A D | 28-Feb-2019 | 17.7 KiB | 643 | 495 |
| cdhit-div.c++ | H A D | 28-Feb-2019 | 2.4 KiB | 70 | 33 |
| cdhit-est-2d.c++ | H A D | 28-Feb-2019 | 3.8 KiB | 116 | 63 |
| cdhit-est.c++ | H A D | 28-Feb-2019 | 3 KiB | 96 | 51 |
| cdhit-utility.c++ | H A D | 28-Feb-2019 | 16.3 KiB | 384 | 361 |
| cdhit-utility.h | H A D | 28-Feb-2019 | 197 | 8 | 6 |
| cdhit.c++ | H A D | 28-Feb-2019 | 2.1 KiB | 69 | 29 |
| clstr2tree.pl | H A D | 03-May-2022 | 958 | 52 | 47 |
| clstr2txt.pl | H A D | 03-May-2022 | 1.2 KiB | 58 | 52 |
| clstr2xml.pl | H A D | 03-May-2022 | 4.4 KiB | 152 | 125 |
| clstr_cut.pl | H A D | 03-May-2022 | 470 | 32 | 25 |
| clstr_list.pl | H A D | 03-May-2022 | 3.2 KiB | 90 | 58 |
| clstr_list_sort.pl | H A D | 03-May-2022 | 1.1 KiB | 52 | 35 |
| clstr_merge.pl | H A D | 03-May-2022 | 3.1 KiB | 145 | 122 |
| clstr_merge_noorder.pl | H A D | 03-May-2022 | 2.1 KiB | 101 | 90 |
| clstr_quality_eval.pl | H A D | 03-May-2022 | 3.4 KiB | 138 | 102 |
| clstr_quality_eval_by_link.pl | H A D | 03-May-2022 | 2.3 KiB | 86 | 55 |
| clstr_reduce.pl | H A D | 03-May-2022 | 1,006 | 52 | 44 |
| clstr_renumber.pl | H A D | 03-May-2022 | 202 | 15 | 12 |
| clstr_rep.pl | H A D | 03-May-2022 | 560 | 33 | 30 |
| clstr_reps_faa_rev.pl | H A D | 03-May-2022 | 1.1 KiB | 58 | 43 |
| clstr_rev.pl | H A D | 03-May-2022 | 1.6 KiB | 84 | 70 |
| clstr_select.pl | H A D | 03-May-2022 | 393 | 30 | 22 |
| clstr_select_rep.pl | H A D | 03-May-2022 | 561 | 39 | 31 |
| clstr_size_histogram.pl | H A D | 03-May-2022 | 785 | 39 | 30 |
| clstr_size_stat.pl | H A D | 03-May-2022 | 731 | 41 | 33 |
| clstr_sort_by.pl | H A D | 03-May-2022 | 812 | 48 | 40 |
| clstr_sort_prot_by.pl | H A D | 03-May-2022 | 1.3 KiB | 60 | 52 |
| clstr_sql_tbl.pl | H A D | 03-May-2022 | 2.9 KiB | 128 | 99 |
| clstr_sql_tbl_sort.pl | H A D | 03-May-2022 | 1.1 KiB | 46 | 38 |
| make_multi_seq.pl | H A D | 03-May-2022 | 1.6 KiB | 77 | 54 |
| plot_2d.pl | H A D | 03-May-2022 | 3.6 KiB | 160 | 126 |
| plot_len1.pl | H A D | 03-May-2022 | 2.1 KiB | 106 | 97 |
README
1For cd-hit
2
3Requirements
4Since 4.8.1, cd-hit supports .gz format input file. This requires zlib library. zlib should
5be install in most Linux systems, so cd-hit should be compiled without issue. If your system
6don't have zlib, please install it first.
7 * On Ubuntu, to install zlib:
8 sudo apt install zlib1g-dev
9 * On CentOS, to install zlib:
10 sudo yum install zlib-devel
11
12
13How to compile
14 1. Compile with multi-threading support (default): make
15 2. Compile without multi-threading support (if you are on very old systems): make openmp=no
16 3. Compile without zlib (if you can not install zlib): make zlib=no
17
18Having problems to compile
19Please contact the author
20
21
22For cd-hit-auxtools
23 cd cd-hit-auxtools
24 make
25
26
27Compile cd-hit on MacOS
28To install CD-HIT on MacOS, first install gcc on your system.
29To use Homebrew (https://brew.sh/), see https://brewformulas.org/gcc.
30Then locate the path to your g++ executable, (e.g. /usr/local/Cellar/gcc/6.3.0_1/bin/g++-6,
31note: yours g++ path is likely to be different), then use command like this:
32 make CC=/usr/local/Cellar/gcc/6.3.0_1/bin/g++-6
33
34
35For psi-cd-hit
36 please download BLAST+ (not legacy BLAST) and install the executables in your $PATH
37
38For more information, please visit http://cd-hit.org
39
40Most up-to-date documents are available at https://github.com/weizhongli/cdhit/wiki
41
42cd-hit is also available as web server, visit http://cd-hit.org for web server address.
43