Claident is a software package for rapid sequence classification (clustering) and accurate taxonomic identification of host organisms of sequences for metabarcoding and DNA barcoding studies.
GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. 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You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. 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Alpha testing release for metabarcoding or barcoding studies. Compressing FASTA in clcleanseqv was completely disabled.
Alpha testing release for metabarcoding or barcoding studies. Illegal arguments in calling VSEARCH were fixed. Error with zero size input files in clcleanseqv was fixed. Compressing FASTA in clcleanseqv was disabled. Eliminating size annotations in clclassseqv was disabled.
Alpha testing release for metabarcoding or barcoding studies. Several new commands for generating BLASTDB were added.
Alpha testing release for metabarcoding or barcoding studies. Several minor bug fixes were applied.
Alpha testing release for metabarcoding or barcoding studies. "clblastdbcmd" and "clmakeblastdb" were added. "Exact" mode was added to "clcleanseqv". Several minor bug fixes were applied.
Alpha testing release for metabarcoding or barcoding studies. An error about "fcopy" was fixed.
Alpha testing release for metabarcoding or barcoding studies. BLAST search problem on Cygwin was fixed.
Alpha testing release for metabarcoding or barcoding studies. A new option "--strand" was added to "clclassseqv", "clcleanseqv" and "clrecoverseqv". Several minor bugs were fixed.
Alpha testing release for metabarcoding or barcoding studies. A new option "--minovllen" was added to "clclassseqv", "clcleanseqv" and "clrecoverseqv". Several minor bugs were fixed.
Alpha testing release for metabarcoding or barcoding studies. New commands "climportfastq", "clconcatpair" and "clmakecachedb" were added. "clclassseqv", "clrecoverseqv", "cldivseq", "clidentseq" and "clcleanseqv" were updated.
Alpha testing release for metabarcoding or barcoding studies. An incompatible problem of "clidentseq" to BLAST+ 2.3.0 was fixed. The QCauto method does not work correctly in previous version with BLAST+ 2.3.0.
Alpha testing release for metabarcoding or barcoding studies. A bug of "clsumclass" was fixed.
Alpha testing release for metabarcoding or barcoding studies. New commands "clcleanseqv", "clclassseqv" and "clrecoverseqv" were added. "clcleanseqv" detects and removes potentially erroneous sequences using VSEARCH based on modified CD-HIT-OTU algorithm. "clclassseqv" clusters denoised sequences and construct OTUs using VSEARCH. "clrecoverseqv" maps raw sequences to OTU sequences and recover potentially erroneous sequences correctly mapped to OTUs. Several commands modified to be compatible to "clcleanseqv", "clclassseqv" and "clrecoverseqv".
Alpha testing release for metabarcoding or barcoding studies. A new command "clmakeuchimedb" which eliminate chimeric sequences from UCHIME reference sequence database was added. A new command "clrunuchime" which perform reference / de novo UCHIME chimera removal implemented in VSEARCH was added. "clshrinkblastdb" was changed to use VSEARCH instead of CD-HIT-EST. "clcleanseq" was changed to use VSEARCH instead of UCHIME. Expelling sequence was disabled in "clclassseq", "clclassclass" and "clreclassclass" by default. "clmaketsv" and "clmakexml" were updated to be compliant with recent DRA specification. "--truncateN" option was added to "clsplitseq". The default parameters of "clidentseq" were changed. "--minalnpcov", "--minalnpcovnn" and "--minalnpcovb" were added to "clidentseq".
Alpha testing release for metabarcoding or barcoding studies. A critical bug of "--trimlowcoverage" option of "clcleanseq", "clclassseq", "clclassclass" and "clreclassclass" was fixed. "--trimlowcoverage" option of "clclassclass" and "clreclassclass" disabled by default.
Alpha testing release for metabarcoding or barcoding studies. "--index1" and "--index2" options were exchanged. The "--otuseq" option of "clfiltersum" was fixed. "--trimlowcoverage" option was added to "clcleanseq", "clclassseq", "clclassclass" and "clreclassclass", and was enabled by default. Several minor bugs were also fixed.
Alpha testing release for metabarcoding or barcoding studies. New commands "clshrinkblastdb" and "clderepblastdb" were added. Several minor bugs were also fixed.
Alpha testing release for metabarcoding or barcoding studies. Install script was modified for non-default install place.
Alpha testing release for metabarcoding or barcoding studies. Several new options were added to "clfiltersum" and "clfilterseq".
Alpha testing release for metabarcoding or barcoding studies. Several minor bugs were fixed. New commands "clfillassign", "clfiltersum" were added. Several default options were changed.
Alpha testing release for metabarcoding or barcoding studies. Several minor bugs were fixed. A new command "clreclassclass" was added.
Alpha testing release for metabarcoding or barcoding studies. The paired-end sequence name problem of "clsplitseq" was fixed.
Alpha testing release for metabarcoding or barcoding studies. Optimized for FASTQ and MiSeq sequence data.
Alpha testing release for metabarcoding or barcoding studies. "clidentseq", "clsumclass", "clcleanseq", "clmaketsv", "clmakexml", "clelimdupgi" and "clmaketaxdb" were refined.
Alpha testing release for metabarcoding or barcoding studies. "cldenoiseseq" was renamed to "clcleanseq" and refined. "clrevcompseq" was refined.
Alpha testing release for metabarcoding or barcoding studies. "cldenoiseseq" was refined.
Alpha testing release for metabarcoding or barcoding studies. Fixed problems on DRA submission. New "cldenoiseseq" command was added.
Alpha testing release for metabarcoding or barcoding studies. Fixed problems on DRA submission.
Alpha testing release for metabarcoding or barcoding studies.