GBrowse syn Scripts

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aln2hit.pl

aln2hit.pl is a generic alignment data parser that will generate a tab-delimited file suitable for loading into the GBrowse_syn alignment database.

Example:

$ perl aln2hit -f clustalw my_alignments.aln >my_alignments.txt
$ perl load_alignment_database -d my_database -u name -p passwd my_alignments.txt

It accepts as input an alignment data file in formats recognized by BioPerl. For best results, use FASTA or CLUSTALW formats, taking care to format the sequence IDs as described [here].

clustal2hit.pl

load_alignment_database.pl

load_alignments_gff3.pl

load_alignments_msa.pl

mercatoraln_to_synhits.pl

split_clustal.pl