####INTRODUCTION: This is the pipeline for carrying out reciprocal BLAST searches and was used in: Warren et al 2014 Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon Genome Biology and Evolution This pipeline is not as smooth as it should be as I was a worse programmer when it was written than I am now. If you need any help or have any queries, drop me an e-mail at ianawarren.work AT gmail.com ####SETUP/SCRIPTS/REQUIREMENTS: This was run on a MacOS 10.8.5 using python 2.7.5 I can't see any reason why it won't run on later versions of the above. It wouldn't take too much modification to run it on a Linux system either The required external scripts/programs are (a google search will locate the source files readily): ##NCBI's BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download ### You also need ian_mods.py installed, as this has some modules used in the main script. ####IMPORTANT All of these programs need to be located somewhere they can be found in the PATH. THis is true for the blast databases as well. ####INPUT FILES: You required: 1) Two fasta files containing the two groups of sequences that are to be searched 2) BLAST databases of the sequences that are to be searched. They need to be in the local directory or their location put into the PATH To run the program just type reciprocalblast_allsteps.py then you will be lead through the prompts. NB It is case sensitive. NB2 It is not possible to do reciprocal BLAST searches using two different types of sequence eg protein vs nucleotide. I play to fix this.