
CD-HIT ChangeLog

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.
