ssu - high-performance phylogenetic diversity calculations

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

ssu 0.10.0                                          July 2021                                             SSU(1)

       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).

       ssu - high-performance phylogenetic diversity calculations