Sequence Manipulation tools
by Joseph Hughes, University of Glasgow
Consensus.pl
Consensus.pl is a perl script which creates consensus sequences from a fasta alignement. This script uses use Bioperl modules.
Usage: Consensus.pl -in - the input alignment in fasta format -out - the directory path for the output consensus in fasta format -t - an optional threshold parameter as a percentage (0-100), so that positions in the alignment with lower percent-identity than the threshold are marked by ? in the consensus -iupac - an optional parameter to make a consensus using IUPAC ambiguity codes from DNA and RNA. -help - Get this help
Example:
perl ../../Script/Consensus.pl -in alignment.fasta -out ../Consensus/consensus.fasta -iupac
It is best to run this from within the directory where you have your alignment so that the identifier of the consensus sequence in the output does not have a path direcotry name.
fastaQual2fastq.pl
A perl script to convert FASTA + QUAL files to FASTQ
Usage: fastaQual2fastq.pl path/to/input/file
The input file must have the extension .fasta or .fna and the associated quality file
must have the same name with extension .qual
Fasta2Phylip.pl
A perl script to convert a fasta file to phylip format for running PHYML or RaxML for example.
Usage: Fasta2Phylip.pl path/to/input/fastafile
SplitFasta.pl
A perl script to split a multiple fasta file into a user specified number of files. Useful for splitting a job to run on multiple threads or server nodes.
Usage: SplitFasta.pl -in path/to/multifastafile -s int
int is the number of files you want it split into.
SelectSeq.pl
A perl script to pull out individual fasta sequences from a multi fasta file based of id matching, description matching, exact id match and randomly selecting a sequence
Usage: SelectSeq.pl -in path/to/multifastafile -out output/file [options]
gb2fa.pl
A perl script that uses bioperl and converts a genbank file containing 1 or more sequences into a multi fasta file.
Usage: gb2fa.pl -in infile.gb -out outfile.fa
fa2oneline.pl
A perl script for converting a fasta file wrapped over multiple lines into a fasta file with the sequence on a single line.
Usage: fa2oneline.pl multiline.fa > oneline.fa