Guidance2

Introduction

GUIDe Tree Based AligNment ConfidencE (GUIDANCE) is a software package for aligning biological sequences (DNA or amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating confidence scores for each column, sequence and residue in the alignment.

For more information, please check:
BioContainers: https://hub.docker.com/repository/docker/arnstrm2/guidance2/general
Home page: https://taux.evolseq.net/guidancever2/source.php

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

BELL

2.02

NEGISHI

2.02

Commands

  • Create_Chimera_Figure_Files_For_ConSurfDB.pl

  • Create_PyMol_Files_For_ConSurfDB.pl

  • HoT_COS_GUIDANCE2.pl

  • Monitor_Bioseq_Node.pl

  • Remove_Pos_bellow_Cutoff.pl

  • Remove_Seq_bellow_Cutoff.pl

  • Replace_B_Factor_With_ConSurf_Grade.pl

  • blastpgp_to_fasta.pl

  • calculate_statistics.pl

  • checkjob.pl

  • cluster.pl

  • code2nameFasta.pl

  • code2nameTree.pl

  • colorCoding.v2.pl

  • colorCodingLinear.pl

  • convertBSTrees2MafftFormat.pl

  • convertNacessFormat.pl

  • create_MSA_from_blast.pl

  • create_chimerx.pl

  • create_colored_chimera_msa.pl

  • daemon.pl

  • extract_info_from_pdb.pl

  • failedCheck.pl

  • guidance.pl

  • isEqualTree

  • maskLowScoreResidues.pl

  • msa_set_score

  • name2codeFastaFrom1.pl

  • printColoredAlignment.pl

  • pullOutBStrees.pl

  • r4s_res_to_gradesPE.pl

  • removeLowSPsites.pl

  • removeTaxa

  • remove_old_results.pl

  • rootTree.pl

  • runAlignBStrees.pl

  • selecton_run_calc.pl

  • semphy

  • sendEmail.pl

  • statTest.pl

  • test_time.pl

  • update_runTime.pl

Module

You can load the modules by:

module load biocontainers
module load guidance2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run guidance2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=guidance2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers guidance2

# Your guidance2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=guidance2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers guidance2

# Your guidance2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=guidance2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers guidance2

# Your guidance2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=guidance2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers guidance2

# Your guidance2 workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=guidance2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers guidance2

# Your guidance2 workflow...