forked from weizhongli/cdhit
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ChangeLog
124 lines (95 loc) · 3.98 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
CD-HIT ChangeLog
CD-HIT-V4.8.1 (2019-03-01):
Add: support .gz input files
CD-HIT-V4.6.8 (2017-06-22):
Add: CD-HIT-OTU-MiSeq is included as an use case, for clustering 16S rDNA MiSeq paired end reads.
Fix: Minor fix made for CD-HIT-OTU-MiSeq
CD-HIT-V4.6.7 (2017-05-02):
Add: cd-hit-est and cd-hit-est-2d now can cluster paired end (PE) reads.
AddL user can select sub-sequence from the beginning of the sequences for clustering.
Add: psi-cd-hit.pl can work with BLAST+
Add: output cluster file can be sorted by cluster size too (cluster length still default)
Add: output fasta file can be sorted by cluster size.
CD-HIT-V4.6.6 (2016-07-12):
Fix: cd-hit-dup in variable length input when write out R1 reads
CD-HIT-V4.6.5 (2016-03-05):
Add filter for -aL option so that short sequences will be skipped if not
satisfy representative sequences' -aL requirement. This will make compute
faster in clustering settings where sequences in the same cluster are
required to have similar length using -aL -AL option (e.g. -aL 0.9).
CD-HIT-V4.6.4 (2015-04-04):
Major update of cd-hit-dup output format: previous cd-hit-dup output trimmed
reads, or merged reads of (R1 and R2) for paired end (PE) reads. The output
are not really useful for later analysis. In this version, the full length
reads are in the output. For PE reads, both full length reads are in the
output files.
CD-HIT-V4.6.3 (2015-05-14):
Fix: A few bug fix
Fix: Updated documents
Add: Makefile, openmp as default
CD-HIT-V4.6.2 (2015-05-06):
Fix: few bug fixes
Add: support for negative value of the -T option
Add: minor improvement for supporting long sequences
Add: new psi-cd-hit-2013-0525, which was developed separately, back to cd-hit
Add: cd-hit-auxtools-v0.5-2012-03-07-fix
CD-HIT-V4.6.1 (2012-08-27):
Fix: a minor bug in handling masking letters;
Add: a few minor changes and fixings to conform to debian packaging rules.
CD-HIT-V4.6 (2012-04-25):
Add: better auto tuning (for -M 0) of word table size for both single and multiple threaded execution;
Fix: a minor bug for very long input sequences;
Add: compiling option to change MAX_SEQ.
CD-HIT-V4.5.8 (2012-03-24):
Add: handling of asterisk at the end of sequences;
Add: a few minor improvements in the parallelization;
Add: new options -mask and -bak.
CD-HIT-V4.5.7 (2011-12-16):
Add: minor improvements to the word table size handling;
Add: updated documentation file.
CD-HIT-V4.5.6 (2011-09-02):
Fix: -M for cd-hit-2d and cd-hit-est-2d;
Fix: handling of invalid input sequences.
CD-HIT-V4.5.5:
Fix: a minor bug in option handling for score setting (-match, -mismatch);
Fix: a minor bug in printing logs to stdout for cd-hit-2d and cd-hit-2d-est.
CD-HIT-V4.5.4:
Add: support for FASTQ file as input;
Add: improvement to sequence partition for parallelization;
Change: default identity threshold from 0.9 to 0.95 for EST.
CD-HIT-V4.5.3:
Add: cd-hit-454 program to the main package (cdhit-454.c++);
Add: options to change the scoring settings;
Add: options to control the length of unmatched region.
CD-HIT-V4.5.2:
MinorChange: default value of "-n" for DNA sequence from 8 to 10;
MinorFix: alignment locations and length;
CD-HIT-V4.5.1:
MinorChange: default value of "-r" from 0 to 1;
MinorFix: alignment length for "-G 0".
CD-HIT-V4.5:
Remove: multi-level counting;
Fix: support for "-F" option.
CD-HIT-V4.5-Beta3:
Change: default word table size for "-M 0";
Fix: global identity computation.
CD-HIT-V4.5-Beta2:
Fix: alignment position and identity.
CD-HIT-V4.5-Beta:
Change: local band alignment;
Change: filter threshold calculation;
Fix: best alignment band searching;
CD-HIT-V4.3:
Fix: a few bugs related to multi-level counting;
Change: implementation for -M option.
CD-HIT-V4.2.x:
Some bug fixings.
CD-HIT-V4.2:
Add: multi-level counting array to improve the speed.
CD-HIT-V4.1.1:
Change: improve estimating alignment band for sequences with low complexity.
CD-HIT-V4.1:
Fix: a bug in searching best alignment band;
Fix: a bug in handling 'N' for EST;
CD-HIT-V4.0:
New implementation with parallelization using OpenMP.