.. _backbone-label:

#######
 Hmmer
#######

**************
 Introduction
**************

Hmmer is used for searching sequence databases for sequence homologs,
and for making sequence alignments.

**********
 Versions
**********

-  3.3.2

**********
 Commands
**********

-  alimask
-  easel
-  esl-afetch
-  esl-alimanip
-  esl-alimap
-  esl-alimask
-  esl-alimerge
-  esl-alipid
-  esl-alirev
-  esl-alistat
-  esl-compalign
-  esl-compstruct
-  esl-construct
-  esl-histplot
-  esl-mask
-  esl-mixdchlet
-  esl-reformat
-  esl-selectn
-  esl-seqrange
-  esl-seqstat
-  esl-sfetch
-  esl-shuffle
-  esl-ssdraw
-  esl-translate
-  esl-weight
-  hmmalign
-  hmmbuild
-  hmmconvert
-  hmmemit
-  hmmfetch
-  hmmlogo
-  hmmpgmd
-  hmmpgmd_shard
-  hmmpress
-  hmmscan
-  hmmsearch
-  hmmsim
-  hmmstat
-  jackhmmer
-  makehmmerdb
-  nhmmer
-  nhmmscan
-  phmmer

*************
 Example job
*************

Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=hmmer       # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load hmmer/XXXX ### Latest version is recommended.