The GUIDANCE2 Server Server for alignment confidence score
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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.

2016, October 26 - releasing version 2.02:
Supporting newer gcc versions (up until version 6.20), minor bugfixes

2015, November 24 - releasing version 2.01:
Minor bugfixes

2014, September 7 - releasing version 2.0:
New and improved GUIDANCE2 algorithm implemeted, see overview for details

2014, August 7 - releasing version 1.5:
Other way to calculate col_col score which account for gap positions, bugfixes

2013, December 22 - releasing version 1.4.1:
Added support for new versions of PRANK and MAFFT, bugfixes

2012, October 24 - releasing version 1.3.1:
Minor bugfixes

2012, October 3 - releasing version 1.3:
Added support for new versions of PRANK, bugfixes

2012, June 22 - releasing version 1.2:
Added support for the new aligner PAGAN, parallelization, reduced running time, bugfixes

2011, May 2 - releasing version 1.1:
Added visualization in Jalview, option for using MUSCLE, improved commandline interface, bugfixes, support more optional alignment parameters

2. Unzip and untar the files:

tar -xzvf guidance.v2.02.tar.gz

This will create a directory named guidance.v2.02

3. Make:

cd guidance.v2.02
make

4. Check if you have the desired alignment program(s) installed:

• MAFFT: Type "mafft" and check that you have version 6.712 or newer.
• Else download and install MAFFT from:
  http://mafft.cbrc.jp/alignment/software/
• PRANK: Type "prank" and check that you have version v.100223 or newer.
• Else download and install PRANK from:
  http://www.ebi.ac.uk/goldman-srv/prank/prank/
• CLUSTALW: Type "clustalw" and check that you have it insalled
  
  • Else download and install CLUSTALW from:
    http://www.ebi.ac.uk/Tools/clustalw2/index.html
  
  

5. GUIDANCE also uses Perl, BioPerl and Ruby:

• Type "perl -v" and check that you Perl installed.
• Else download and install it from:
  http://www.perl.org/
• Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.
• Else download and install it from:
  http://www.bioperl.org/
• Type "ruby --version" to check that you have ruby.
• Else download and install it from:
  http://www.ruby-lang.org/en/

For any problems - please contact us
Guidance Source Code in Github

Running GUIDANCE
Run the Perl script: guidance/www/Guidance/guidance.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: "perl guidance.pl")

USAGE: perl <guidance directory>/www/Guidance/guidance.pl --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW|MUSCLE] --seqType [aa|nuc|codon] --outDir FULL_PATH_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 [please provid full (and not relative) path]

Optional parameters:
--program [GUIDANCE2|GUIDANCE|HoT] Default=GUIDANCE2
--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
--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 directory>/www/Guidance/guidance.pl --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir /somewhere/protein.guidance
  - will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory "/somewhere/protein.guidance"


• perl <guidance directory>/www/Guidance/guidance.pl --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir /somewhere/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 "/somewhere/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 evolseq@tauex.tau.ac.il.
Enjoy!