ssu1
High-performance phylogenetic diversity calculations
Overview
usage: ssu -i <biom> -o <out.dm> -m [METHOD] -t <newick> [-n threads] [-a alpha] [--vaw]
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[--mode [MODE]] [--start starting-stripe] [--stop stopping-stripe] [--partial-pattern <glob>] [--n-partials number_of_partitions] [--report-bare]
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-i -
The input BIOM table.
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-t -
The input phylogeny in newick.
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-m -
The method, [unweighted | weighted_normalized | weighted_unnormalized | generalized].
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-o -
The output distance matrix.
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-n -
[OPTIONAL] The number of threads, default is 1.
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-a -
[OPTIONAL] Generalized UniFrac alpha, default is 1.
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-f -
[OPTIONAL] Bypass tips, reduces compute by about 50%.
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--vaw -
[OPTIONAL] Variance adjusted, default is to not adjust for variance.
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--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.
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--start -
[OPTIONAL] If mode==partial, the starting stripe.
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--stop -
[OPTIONAL] If mode==partial, the stopping stripe.
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--partial-pattern -
[OPTIONAL] If mode==merge-partial, a glob pattern for partial outputs to merge.
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--n-partials -
[OPTIONAL] If mode==partial-report, the number of partitions to compute.
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--report-bare -
[OPTIONAL] If mode==partial-report, produce barebones output.
Citations:
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For UniFrac, please see:
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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
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For Generalized UniFrac, please see:
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Chen et al. Bioinformatics 2012; DOI: 10.1093/bioinformatics/bts342
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For Variance Adjusted UniFrac, please see:
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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).
Releases
5 releases since Debian 3.0 (Woody); the text changed 3 times.
--mode since Debian 12 (Bookworm);
--n-partials since Debian 12 (Bookworm);
--partial-pattern since Debian 12 (Bookworm);
--report-bare since Debian 12 (Bookworm);
--start since Debian 12 (Bookworm);
--stop since Debian 12 (Bookworm);
--vaw since Debian 12 (Bookworm);
-a since Debian 12 (Bookworm);
-f since Debian 3.1 (Sarge);
-i since Debian 12 (Bookworm);
-m since Debian 3.1 (Sarge);
-n since Debian 12 (Bookworm);
-o since Debian 12 (Bookworm);
-t since Debian 12 (Bookworm).
-c until Debian 4.0 (Etch);
-l until Debian 4.0 (Etch).