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.
tar -xzvf guidance.v2.02.tar.gz
cd guidance.v2.02
make
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)
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 directory "/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 directory
"/somewhere/codingSeq.guidance". Only 30 bootstrap iterations will be done instead of the
default 100 (cut run-time by a factor of 3)