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.