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README.txt 2012-11-13 1.0 kB
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single_linkage.pl v1.01 Perl script for single linkage clustering using output produced from blast or uclust all against all 
Copyright (C) 2012  Douglas Chesters
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License

invokes unix commands rm and sort. therefore, only runs under linux, and probably mac.

input is list of pairwise distances. in this format:

query	target	evalue	id	cols
ILG1N3N4Ca5An7tex_JQ568362	ILG1N3N4Ca5An7tex_JQ568362	0	100.0	658
ILG1N3N4Ca5An7tex_JQ568362	ILG1N3N4Ca5An7texana_JN806443	0	96.4	642

heres how you can calculate these pw distances using blast+:

makeblastdb -in seqs.fas -dbtype nucl
blastn -db seqs.fas -out current_distances -evalue 1e-5 -query seqs.fas -num_alignments 10000 -num_descriptions 10000 -outfmt '6 sseqid qseqid evalue pident length'

and heres the command for uclust:
usearch --query seqs.fas --db seqs.fas --userout current_distances2 --userfields query+target+evalue+id+cols --evalue 1e-5 --nousort
Source: README.txt, updated 2012-11-13