@weizhongli weizhongli released this Jun 21, 2017 · 17 commits to master since this release

Assets 4

CD-HIT-OTU-MiSeq is included as an use case, for clustering 16S rDNA MiSeq paired end reads.
Minor fix made for CD-HIT-OTU-MiSeq in cd-hit-v4.6.8-2017-1208-source.tar.gz

@weizhongli weizhongli released this May 1, 2017 · 36 commits to master since this release

Assets 4

cd-hit-est and cd-hit-est-2d now can cluster paired end (PE) reads.
user can select sub-sequence from the beginning of the sequences for clustering.
psi-cd-hit.pl can work with blast+.
output cluster file can be sorted by cluster size, in addition to cluster length, which is still the default
output fasta file can be sorted by cluster size.

@weizhongli weizhongli released this Jul 12, 2016 · 85 commits to master since this release

Assets 3

Bug fix for cd-hit-dup in variable length input when write out R1 reads

@weizhongli weizhongli released this Mar 4, 2016 · 86 commits to master since this release

Assets 3

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).

@weizhongli weizhongli released this Jun 3, 2015 · 88 commits to master since this release

Assets 3

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.

@weizhongli weizhongli released this May 13, 2015 · 90 commits to master since this release

Assets 3

A few bug fix
Updated documents
Makefile, openmp as default
Support for negative value of the -T option
Add a minor improvement for supporting long sequences
Add new psi-cd-hit-2013-0525, which was developed separately, back to cd-hit
cd-hit-auxtools-v0.5-2012-03-07-fix was added to cd-hit

Pre-release

@weizhongli weizhongli released this May 6, 2015 · 97 commits to master since this release

Assets 3

A few bug fix
Support for negative value of the -T option
Add a minor improvement for supporting long sequences
Add new psi-cd-hit-2013-0525, which was developed separately, back to cd-hit
cd-hit-auxtools-v0.5-2012-03-07-fix was added to cd-hit

@weizhongli weizhongli released this May 5, 2015

Assets 3

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.