---
name: "psi-cd-hit-2d"
section: "1"
platform: "linux"
package: "cd-hit"
version: "4.6.1-2012-08-27-2"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/psi-cd-hit-2d"
---

# psi-cd-hit-2d(1)

runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format

## NAME

psi-cd-hit-2d.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format

## DESCRIPTION

Usage psi-cd-hit-2d \[Options\]

Options

- **-i**

  in\_dbname, required

- **-o**

  out\_dbname, required

- **-c**

  clustering threshold (sequence identity), default 0.3

**-ce** clustering threshold (blast expect), default **-1**,

-

  it means by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either identity threshold or expect threshold

- **-L**

  coverage of shorter sequence ( aligned / full), default 0.0

- **-M**

  coverage of longer sequence ( aligned / full), default 0.0

- **-R**

  (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search

- **-G**

  (1/0) use global identity? default 1 sequence identity calculated as

-

  total identical residues of local alignments / length of shorter seq

-

  if you prefer to use **-G** 0, it is suggested that you also use **-L**, such as **-L** 0.8, to prevent very short matches.

- **-d**

  length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space

- **-l**

  length\_of\_throw\_away\_sequences, default 10

- **-p**

  profile search para, default

-

  "-a 2 **-d** nr80 **-j** 3 **-F** F **-e** 0.001 **-b** 500 **-v** 500"

**-bfdb** profile database, default nr80

- **-s**

  blast search para, default

-

  "-F F **-e** 0.000001 **-b** 100000 **-v** 100000"

**-be** blast expect cutoff, default 0.000001

- **-b**

  filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts

**-pbs** No of jobs to send each time by PBS querying system

-

  you can not use both ssh and pbs at same time

**-k** (1/0) keep blast raw output file, default 1

**-rs** steps of save restart file and clustering output, default 5000

-

  everytime after process 5000 sequences, program write a restart file and current clustering information

**-restart** restart file, readin a restart file

-

  if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"

**-rf** steps of re format blast database, default 200,000

-

  if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time

**-local** dir of local blast db,

-

  when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY NOT FASTER

- **-J**

  job, job\_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself

**-single** files of ids those you known that they are singletons

-

  so I won't run them as queries

**-i2** second input database

**-blastn** run blastn, default 0

**-lo** how long can seq in db2 \> db1 in a cluster, default 0

-

  means, that seq in db2 should \<= seqs in db1 in a cluster

-

  \============================== by Weizhong Li, liwz@sdsc.edu ==============================

-

  If you find cd-hit useful, please kindly cite:

-

  "Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam GodzikBioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam Godzik Bioinformatics, (2006) 22:1658-1659