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SNP Sites
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This program finds snp sites from a multi fasta alignment file.
Usage: snp_sites [-mvph] [-o output_filename] <file>
This program finds snp sites from a multi fasta alignment file.
-m output a multi fasta alignment file (default)
-v output a VCF file
-p output a phylip file
-o specify an output filename
-h this help message
<file> input alignment file which can optionally be gzipped
This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:
a multi fasta alignment,
VCF,
relaxed phylip format.
Example usage:
snp_sites my_alignment.aln
snp_sites my_gzipped_alignment.aln.gz
Multi Fasta Alignment
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Similar to the input file but just containing the SNP sites.
VCF
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This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.
Relaxed Phylip format
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All the SNP sites in a format for RAxML and other tree building applications.