MitoNuc

Evan McCartney-Melstad

This is a set of tools that will be used to do a few things:

• make many subsets of NCBI databases
• run clustering analyses on these sub-databases
• run phylogenetic analyses on the resulting nucleotide/protein clusters

This software was written on a Linux machine. It should work cross-platform, however, as long as Perl, BioPerl, BioPerl-run, and blast+2.2.27 are installed and configured correctly. See below for some tips on that.

MitoNuc requires several things to function. Among these are:

• BioPerl-live (latest version of BioPerl from GitHub)
• BioPerl-run (latest version from GitHub)
• blast+2.2.27
• Perl needs to know where to find the bioperl-run and bioperl-live modules
  • can do this by modifying the $PERL5LIB environmental variable
  • for instance: export PERL5LIB="$HOME/bioperl/bioperl-live:$HOME/bioperl/bioperl-run/lib:$PERL5LIB"
• Perl needs to know where to find the blast+ binaries
  • do this by setting the $BLASTPLUSDIR environmental variable
• Perl needs to know where to find the blast(+) databases
  • must set the $BLASTDB environmental variable to point to the databases (which you must download)