---
name: "ssu"
section: "1"
platform: "linux"
package: "unifrac-tools"
version: "1.4-3+b4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ssu"
---

# ssu(1)

high-performance phylogenetic diversity calculations

## 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.