NAME

       ssu - high-performance phylogenetic diversity calculations

DESCRIPTION

       usage: ssu -i <biom> -o <out.dm> -m [METHOD] -t <newick> [-n threads] [-a alpha] [--vaw]

              [--mode     [MODE]]     [--start    starting-stripe]    [--stop    stopping-stripe]
              [--partial-pattern <glob>] [--n-partials number_of_partitions] [--report-bare]

       -i     The input BIOM table.

       -t     The input phylogeny in newick.

       -m     The  method,  [unweighted   |   weighted_normalized   |   weighted_unnormalized   |
              generalized].

       -o     The output distance matrix.

       -n     [OPTIONAL] The number of threads, default is 1.

       -a     [OPTIONAL] Generalized UniFrac alpha, default is 1.

       -f     [OPTIONAL] Bypass tips, reduces compute by about 50%.

       --vaw  [OPTIONAL] Variance adjusted, default is to not adjust for variance.

       --mode [OPTIONAL]  Mode  of  operation:  one-off  :  [DEFAULT] compute UniFrac.  partial :
              Compute UniFrac over  a  subset  of  stripes.   partial-report  :  Start  and  stop
              suggestions for partial compute.  merge-partial : Merge partial UniFrac results.

       --start
              [OPTIONAL] If mode==partial, the starting stripe.

       --stop [OPTIONAL] If mode==partial, the stopping stripe.

       --partial-pattern
              [OPTIONAL] If mode==merge-partial, a glob pattern for partial outputs to merge.

       --n-partials
              [OPTIONAL] If mode==partial-report, the number of partitions to compute.

       --report-bare
              [OPTIONAL] If mode==partial-report, produce barebones output.

   Citations:
              For UniFrac, please see:

              McDonald  et  al.  Nature Methods 2018; DOI: 10.1038/s41592-018-0187-8 Lozupone and
              Knight Appl Environ Microbiol 2005; DOI: 10.1128/AEM.71.12.8228-8235.2005  Lozupone
              et  al.  Appl  Environ Microbiol 2007; DOI: 10.1128/AEM.01996-06 Hamady et al. ISME
              2010;   DOI:   10.1038/ismej.2009.97   Lozupone   et   al.    ISME    2011;    DOI:
              10.1038/ismej.2010.133

              For Generalized UniFrac, please see:

              Chen et al. Bioinformatics 2012; DOI: 10.1093/bioinformatics/bts342

              For Variance Adjusted UniFrac, please see:

              Chang et al. BMC Bioinformatics 2011; DOI: 10.1186/1471-2105-12-118

       Runtime  progress  can  be  obtained by issuing a SIGUSR1 signal. If running with multiple
       threads, this signal will only be honored if issued to the master PID.   The  report  will
       yield the following information:

       tid:<thread  ID>  start:<starting  stripe> stop:<stopping stripe> k:<postorder node index>
       total:<number of nodes>

       The proportion of the tree that has been evaluated can be determined from (k / total).

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.