ssu - high-performance phylogenetic diversity calculations
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.
- 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).
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.