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SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes.

This code requires:
Bio::SeqIO;
Bio::Perl;
Bio::Tools::Run::StandAloneBlast;
Bio::Seq;
Bio::Tools::Blast;
Bio::DB::GenBank;
Bio::DB::WebDBSeqI;

and BLAST 2.2.28 (blastall and formatcmd)  installed and reachable from your command line

Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment identity threshold in %>

OR 

Usage: perl SimplyTheBlast-Evalue.pl <fasta formatted seeds file> <path to genomes folder> <Evalue threshold> 

Genomes files names must end with *.faa

Output files:

TABULAR_FBH_OUTPUT.xls is an Excel readable file with the identifier (everything is in the sequence name until the first "\s" character) of the best hits found in each genome for each query sequence 
TABULAR_FBH_OUTPUT.csv is a csv file  with the number of the best hits found in each genome for each query sequence (this file can be imported in R for heatmap construction)
query_n* files are fasta formatted files with the sequences of the best hits found in each genome for each query sequence.

bugs or comments to:
marco.fondi@unifi.it 
mrcfnd@gmail.com
Source: README, updated 2014-11-14