Source Code


Please note that the GUIDANCE source code is freely distributed for academic use only (see copyrights statement below)
1. Downloading and compiling GUIDANCE.
2. Running GUIDANCE

Downloading and Compiling GUIDANCE
The following instructions should work right out of the box for UNIX-like systems. Mac should also work in principle, but is not yet supported. Windows will require some additional work, such as setting up a cygwin environment.

1. Download the GUIDANCE source code.
2. Unzip and untar the files:

tar -xzvf guidance.v1.01.tgz

This will create a directory named guidance.v1.01

3. Make:

cd guidance.v1.01
make

4. Check if you have the desired alignment program(s) installed:
5. GUIDANCE also uses Perl and BioPerl:
  • Type "perl -v" and check that you Perl installed.
  • Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.

For any problems - please contact us

 Running GUIDANCE
Run the Perl script: guidance/www/Guidance/run_calc.pl
(Note that you cannot move this script out of its directory, because it uses relative paths to other files in other directories. Sorry)
GUIDANCE uses flags in the command line arguments: (for help, type: "guidance")

USAGE: guidance --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW] --seqType [aa|nuc|codon] --outDir OUTDIR

Required parameters:
--seqFile: Input sequence file in FASTA format
--msaProgram: Which MSA program to use
--seqType: Type of sequences for alignment (amino acids, nucleotides, or codons)
--outDir: Output directory that will be created automatically and hold all output files

Optional parameters:
--program [GUIDANCE|HoT] Default=GUIDANCE
--bootstraps: Number of bootstrap iterations (only for GUIDQANCE). Defaut=100
--genCode: Genetic code identifier (only for codon sequences). 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 [aligned|as_input] default=aligned
--msaFile: Input alignment file - not recommended, see the overview section
--seqCutoff: Confidence cutoff between 0 to 1. Default=0.6
--colCutoff: Confidence cutoff between 0 to 1. Default=0.93
--mafft: path to mafft executable. Default=mafft
--prank: path to prank executable. Default=prank

EXAMPLES:
  • guidance --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir protein.guidance
    - will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory "protein.guidance"

  • guidance --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir 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 "codingSeq.guidance". Only 30 bootstrap iterations will be done instead of the default 100 (cut run-time by a factor of 3)


For any problems or questions please contact us at bioSequence@tauex.tau.ac.il.
Enjoy!

Copyrights:
  • To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko
  • Please note that the use of the GUIDANCE program is for academic use only