GUIDANCE v2.0.2:
GUIDe Tree Based AligNment ConfidencE

Authors:

Osnat Penn
Eyal Privman
Haim Ashkenazy
Itamar Sela
Giddy Landan
Dan Graur
Tal Pupko

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.

Citations

GUIDANCE2 (please cite when used):

• Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015) GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research, 2015 Jul 1; 43: W7-W14.; doi: 10.1093/nar/gkq443

• Landan, G., and D. Graur. (2008). Local reliability measures from sets of co-optimal multiple sequence alignments. Pac Symp Biocomput 13:15-24

GUIDANCE (please cite when used)

• Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. (2010). An alignment confidence score capturing robustness to guide-tree uncertainty. Molecular Biology and Evolution, 2010 Aug;27(8):1759-67; doi:10.1093/molbev/msq066

HoT (please cite when used)

• Landan, G., and D. Graur. (2008). Local reliability measures from sets of co-optimal multiple sequence alignments. Pac Symp Biocomput 13:15-24

Installation

1. Unpack the archive.

   $ tar -xzf guidance.v2.01.tgz

2. Compile the package.

   $ cd guidance.v2.01
   $ make
   # Running `make' takes a while

3. Set <path/to/guidance>/guidance/www/Guidance in the $PATH environment variable in your .bash_profile.

4. Check for the external dependencies.

• BioInformatics:

  • MAFFT: Type "mafft" and check that you have version 6.712 or newer.
  • PRANK: Type "prank" and check that you have it insalled.
  • CLUSTALW: Type "clustalw" and check that you have it insalled.
  • MUSCLE: Type "muscle" and check that you have it insalled.
  • PAGAN: Type "pagan" and check that you have it installed.
    • In case PAGAN is used not for user provided alignment (using --msaFile), mafft is also required to be installed.

• Other Languages:

  • Perl: Type "perl -v" and check that you Perl installed.
  • BioPerl: Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.
  • Ruby: Type "ruby -version" to check that you have ruby.

Usage

Notes:

* Guidance scripts use relative paths. Please do not move them out of their packaged directories.

* GUIDANCE uses flags in the command line arguments

* For help, type: "perl guidance"

Usage with Required Parameters:

$ perl guidance --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW|MUSCLE] --seqType [aa|nuc|codon] --outDir FULL_PATH_OUTDIR

Help Information:

Required parameters:
  --seqFile          Input sequence file in FASTA format
  --seqType      Sequence type may be either of: nuc (nucleotides), aa (amino acids),
                 or codon (nucleotides that will be treated as whole codons)
  --msaProgram   The alignment program - may be either MAFFT, PRANK, CLUSTALW or  MUSCLE
  --outDir       The output directory were all output files will be created [please provide full and not relative path]
                 (will be created automatically)

Optional parameters:
  --program      The confidence measure may be GUIDANCE2, GUIDANCE or HoT. default=GUIDANCE2
  --bootstraps   Number of bootstrap iterations. default=100
  --genCode      Genetic code for use in codon sequence. default=1
                 1>  Nuclear Standard
                 15> Nuclear Blepharisma
                 6>  Nuclear Ciliate
                 10> Nuclear Euplotid
                 2>  Mitochondria Vertebrate
                 5>  Mitochondria Invertebrate
                 3>  Mitochondria Yeast
                 13> Mitochondria Ascidian
                 9>  Mitochondria Echinoderm
                 14> Mitochondria Flatworm
                 4>  Mitochondria Protozoan
  --outOrder     May be either aligned or as_input. default=aligned
  --msaFile      Input alignment file - not recommended, see documentation online at: guidance.tau.ac.il
  --seqCutoff    Sequence confidence cutoff between 0 to 1. default=0.6
  --colCutoff    Columnd confidence cutoff between 0 to 1. default=0.93
  --mafft        Path to mafft executable. default=mafft
  --prank        Path to prank executable. default=prank
  --clustalw     path to clustalw executable. default=clustalw
  --muscle       path to muscle executable. default=muscle
  --pagan        path to pagan executable. default=pagan
  --ruby         path to ruby executable. default=ruby
  --dataset      Unique name for the Dataset - will be used as prefix to outputs (default=MSA)
  --MSA_Param:   Passing parameters for the alignment program e.g -F to prank. To pass parameter containning '-' in it, add \ before each '-' e.g. \-F for PRANK
  --proc_num:    Number of processors to use (default=1)

EXAMPLES:

$ perl guidance.pl --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir /somedir/protein.guidance
# Will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory 
# "/somedir/protein.guidance"

$ perl guidance.pl --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir /somedir/codingSeq.guidance --genCode 2 --bootstraps 30
# Will align the codon sequences in the fasta file "codingSeq.fas" using PRANK after translation using the vertebrate 
# mitochondrial genetic code and output all results to the diretory "/somedir/codingSeq.guidance". Only 30 bootstrap iterations 
# will be done instead of the default 100 (cut run-time by a factor of 3)

Copyrights

* To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: talp@post.tau.ac.il
* Please note that the use of the GUIDANCE program is for academic use only