The RELINDEL server
Confidence score for indels in multiple sequence alignment
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Source Code


Please note that the RELINDEL source code is freely distributed for academic use only (see copyrights statement below)


1. Downloading and compiling RELINDEL.
2. Running RELINDEL

Downloading and Compiling RELINDEL
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 RELINDEL source code.
2. Unzip and untar the files:

tar -xzvf relindel.v1.0.tar.gz

This will create a directory named relindel.v1.0

3. Make:

cd relindel.v1.0
make

4. Check if you have the desired alignment program(s) installed:
5. RELINDEL also uses Perl, BioPerl and Ruby:
For any problems - please contact us

Running RELINDEL
Run the Perl script: relindel.v1.0/programs/relindel/relindel.pl
(Note that you cannot move this script out of its directory, because it uses relative paths to other files in other directories. Sorry)
RELINDEL uses flags in the command line arguments: (for help, type: "perl relindel.pl")

USAGE: perl <relindel directory>/programs/relindel/relindel.pl --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW|MUSCLE|PAGAN|CLUSTALO] --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:
--bootstraps: Number of bootstrap iterations (defaut=100).
--genCode: Genetic code identifier (only for codon sequences). Default=1
--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).
--clustal_omega: path to clustal_omega executable (deafult=clustalo).
--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).
--IndelCutoff: Cutoff for filtering un-reliable indels (default=1)
--MaskStartEndIndels: If used, RELINDEL will ignore indels that reside at either the 3' or the 5' of the input sequence


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



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