cdhit

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I am reading the code of cd-hit-common.c++ and I am puzzled by its aa2idx array: ``` int aa2idx[] = {0, 2, 4, 3, 6, 13,7, 8, 9,20,11,10,12, 2,20,14, 5, 1,15,16,20,19,17,20,18,...

kad-ecoli

Hi cd-hit developers, I am using your tool on metatranscriptomic data. I run the deduplication step after the quality filtering step (i.e. adapter/end trimming with Trimmomatic). Such a procedure usually...

domenico-simone

I used the -p option to print alignment overlap in .clstr file. In some clusters I got the desired information but very often I got: > Cluster 3185 > 0...

isana18

do not override users compiler and compiler flags use CXX instead CC variable because we need a C++ compiler do not force optimization if user has some CXXFLAGS already in...

mmokrejs

Hi, there is http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual but it seems there is no documentation like this in current cd-hit tree (4.6.5). Further, there used to be http://weizhong-lab.ucsd.edu/softwares/cd-hit-454/cdhit-cluster-consensus-2013-03-27.tgz but I don't see it in...

mmokrejs

cd-hit-dup error Assertion `len >= min' failed.

2

Hi, I get the following error when I run cd-hit-dup on the command line with the attached sample fastq file (using the default parameter settings : # Total number of...

audreymannion

Segmentation fault problem

4

Dear all, I had a error message when i process cd-hit-est-2d(CD-HIT, V4.6 (+OpenMP)) on Ubuntu 14.04.3 LTS(GNU/Linux 3.13.0-55-generic x86_64) ,Here shows below: Command:./cd-hit-est-2d -i ~/vp_4/cdhit/mcvv_genes_edit.fasta -i2 ~/vp_4/vibiro_ref/vvgenesad -c 0.99 -n...

victor0104

cannot install CD-HIT

3

``` Dear Weizhing Li's Group and other users, I have downloaded varies versions of your program to my 32bit Win7 operation system but failed in installation. After downloading the program...

GoogleCodeExporter

Trouble Installing CD HIT v4.6.4 on MAC OSX

3

I'm having trouble installing CD HIT v4.6.4 on my MAC OSX (ver. 10.9.4). When I use the "make" command from within the CD-HIT directory I get the following error message:...

parmbruster

``` What steps will reproduce the problem? 1.Download attached file 2.Run cd-hit-v4.6.1-2012-08-27/cd-hit -c .8 -i ARO5000194.fa -o cdhit/ARO5000194 3. What is the expected output? What do you see instead? I...

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