NAME

       proteinortho5 - orthology detection tool

SYNOPSIS

       proteinortho5 [OPTIONS] FASTA1 FASTA2 [FASTA...]

DESCRIPTION

       Proteinortho  is a stand-alone tool that is geared towards large datasets and makes use of
       distributed computing techniques  when  run  on  multi-core  hardware.  It  implements  an
       extended  version  of the reciprocal best alignment heuristic. Proteinortho was applied to
       compute orthologous proteins in the complete set of all 717 eubacterial genomes  available
       at NCBI at the beginning of 2009. Authors succeeded identifying thirty proteins present in
       99% of all bacterial proteomes.

OPTIONS

       -e=    E-value for blast [default: 1e-05]

       -p=    blast program {blastn|blastp|blastn+|blastp+} [default: blastp+]

       -project=
              prefix for all result file names [default: myproject]

       -synteny
              activate PoFF extension to separate similar  sequences  by  contextual  adjacencies
              (requires .gff for each .fasta)

       -dups= PoFF:  number  of  reiterations  for adjacencies heuristic, to determine duplicated
              regions (default: 0)

       -cs=   PoFF: Size of a maximum common substring (MCS) for adjacency matches (default: 3)

       -alpha=
              PoFF: weight of adjacencies vs. sequence similarity (default: 0.5)

       -desc  write description files (for NCBI FASTA input only)

       -keep  stores temporary blast results for reuse

       -force forces recalculation of blast results in any case

       -cpus= number of processors to use [default: auto]

       -selfblast
              apply selfblast, detects paralogs without orthologs

       -singles
              report singleton genes without any hit

       -identity=
              min. percent identity of best blast hits [default: 25]

       -cov=  min. coverage of best blast alignments in % [default: 50]

       -conn= min. algebraic connectivity [default: 0.1]

       -sim=  min. similarity for additional hits (0..1) [default: 0.95]

       -step= 1 -> generate indices 2 -> run  blast  (and  ff-adj,  if  -synteny  is  set)  3  ->
              clustering 0 -> all (default)

       -blastpath=
              path to your local blast (if not installed globally)

       -verbose
              keeps you informed about the progress

       -clean remove all unnecessary files after processing

       -graph generate .graph files (pairwise orthology relations)

       -debug gives detailed information for bug tracking

       More specific blast parameters can be defined by

       -blastParameters='[parameters]' (e.g. -blastParameters='-seg no')

       In case jobs should be distributed onto several machines, use

       -startat=    File number to start with (default: 0)

       -stopat=     File number to end with (default: -1)