NAME

       proteinortho6 - orthology detection tool

SYNOPSIS

       proteinortho6 [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
              {blastp+|blastn+|tblastx+|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn}
              [default: diamond]

       -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)

       -binpath=
              path to your local blast/diamond/... (if not installed globally)

       -verbose
              keeps you informed about the progress

       -clean remove all unnecessary files after processing

       -debug gives detailed information for bug tracking

       More specific blast parameters can be defined by

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

       In case jobs should be distributed onto several machines, use

       -jobs=M/N    If you want to involve multiple machines or separate a Proteinortho run into smaller chunks,
       use  the  -jobs=M/N  option. First, run 'proteinortho6.pl -steps=1 ...' to generate the indices. Then you
       can run 'proteinortho6.pl -steps=2 -jobs=M/N ...' to run small chunks separately.  Instead  of  M  and  N
       numbers  must  be  set  representing  the  number of jobs you want to divide the run into (M) and the job
       division to be performed by the process.