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.

ssu 0.10.0                                          July 2021                                             SSU(1)