PhymmBL

PhymmBL is software for taxonomic classification of metagenomic short reads.[1][2]

Prerequisites

Uses NCBI BLAST

module load ncbi-blast

Installation

PhymmBL installs only in its own directory, downloading all data into "hidden" directories named:

.blastData .genomeData .taxonomyData

To install:

[juser@proteusa01 ~]$ mkdir phymmbl [juser@proteusa01 ~]$ cd phymmbl [juser@proteusa01 phymmbl]$ wgethttp://www.cbcb.umd.edu/software/phymm/phymmbl_installer.tar.gz [juser@proteusa01 phymmbl]$ tar xf phymmbl_installer.tar.gz

This creates 4 Perl scripts, and several "hidden" directories -- do "ls -la" to see them.

To install:

[juser@proteusa01 phymmbl]$ ./phymmblSetup.pl

and follow the prompts.

References

[1] PhymmBL web site

[2] Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models, Brady A., Salzberg, S.L., Nat Methods. 2009 Sep;6(9):673-6,