Parapipe Files

#### PARAPIPE version 2.0 #####

A Perl tool for orthologous sequences detection across a set of genomes. This tool iteratively launches Inparanoid and Multiparanoid softwares on a set of genomes and outputs FASTA sequences of core, accessory and uniques genomes.

Usage: perl Parapipe2.pl

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To run Parapipe, extract the tar archive with 
tar -xvf Parapipe2.0.pl 
then place your genomes in "Parapipe2/genomes" folder. Genomes must be in fasta format and have *.faa extension. 
from the Parapipe2/bin folder execute 

perl parapipe2.pl (all the genomes in the Parapipe2/genomes folder will be analyzed, provided that they end with .faa)


Three sample genomes are already present in the folder Parapipe2/genomes. This folder must contain ONLY the files you want to analyze so remove any other file (but not folder) before launching the tool.

Outputs are stored in the parapipe/bin folder. Ouput consists of  fasta files containing the sets of genese for core, accessory and unique genomes.  A conversion table is also generated, linking original fasta file names to the one number code used by parapipe.

for bugs or questions: 
marco.fondi at unifi.it 
mrcfnd at gmail.com

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