Scripts to convert between different file formats.

Converts the standard output of BRATNextGen (http://www.helsinki.fi/bsg/software/BRAT-NextGen/) to the tabular output.

Usage: BratStandardtoTabular.py [inputfile] [outputfile]

Converts EMBL annotation format to BED format (note score is automatically 1000).

Usage: EMBLtoBED.py [emblfile]

Converts EMBL annotation header to GFF format. Also requires the core genome alignment with the "reference" genome as the first sequence".

Usage: EMBLtoGFF.py [emblfile] [alignment]

Reverse complements entries in a fasta file (can contain multiple records)

Requirements: Python 2.7.3, Biopython 1.63

Usage: FastaReverseComplement.py [inputfile] [outputfile]

Converts a fasta format alignment to a non-interleaved nexus format alignment.

Requirements: Biopython (http://biopython.org/)

Current Versions: Python 2.7.3, Biopython 1.63

Usage: FastaToNexus.py [inputfile] [outputfile]

Converts a fasta format alignmnent to an interleaved nexus format alignment.

Requirements: Biopython

Usage: FastaToNexusInterleaved.py [inputfile] [outputfile]

Converts a fasta format alignment to a sequential phylip format alignment.

Requirements: Biopython

Usage: FastaToPhylip.py [inputfile] [outputfile]

Converts SNP table from Kodon to input for LDhat. This script has not been tested recently.

Usage: KodonToLDhat.py [inputfile] [outputfile prefix] [reference name] [N or ALL]

Converts SNP table from Kodon to Nexus format alignment. This script has not been tested recently.

Usage: Usage: KodonToNexus.py [input file] [outputfile] [name of reference sequence] [N or ALL]

Converts SNP table from Kodon to Phylip format alignment. This script has not been tested recently.

Usage: KodonToPhylip.py [inputfile] [outputfile] [namefile] [number of sequences] [number of nucleotides in alignment]

Replaces reference allele with a '-' in the VCF output from snp-sites at sites where the is a gap in the alignment.

Requirements: Biopython (http://biopython.org/)

Current Versions: Python 2.7.3, Biopython 1.63

Usage: gappedVCF.py [vcf] [fasta]