---
name: "phylonium"
section: "1"
platform: "linux"
package: "phylonium"
version: "1.7-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/phylonium"
---

# phylonium(1)

rapidly estimate evolutionary distances

## NAME

phylonium - rapidly estimate evolutionary distances

## SYNOPSIS

**phylonium** \[*OPTIONS...*\] *FILES*...

## DESCRIPTION

**phylonium** estimates the evolutionary distance between closely related genomes. For this **phylonium** reads the input sequences from *FASTA* files and computes the pairwise evolutionary distance. All sequences in one file are considered to be contigs of the same genome.

## OUTPUT

The output is a symmetrical distance matrix in *PHYLIP* format, with each entry representing divergence with a positive, real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases *nan* is printed. This either means that the input sequences were too short (\<200bp) or too diverse (K\>0.5) for our method to work properly.

## OPTIONS

- **-2**, **--2pass**

  After a first run a 'central' sequence is chosen as reference for the second pass. This improves the accuracy when the first reference is an outgroup.

- **-b** *INT*, **--bootstrap**=*INT*

  Compute multiple distance matrices, with *n-1* bootstrapped from the first. See the paper Klötzl & Haubold (2016) for a detailed explanation.

- **-r** *FILE*

  Define the reference sequence.

- **-t** *INT*, **--threads**=*INT*

  The number of threads to be used; by default, all available processors are used.\
   Multithreading is only available if **phylonium** was compiled with OpenMP support.

- **-p** *FILE*

  Print the reference positions to the given path. Also sets complete deletion.

- **--progress**\[=*WHEN*\]

  Print a progress bar. *WHEN* can be 'auto' (default if omitted), 'always', or 'never'.

- **-v**, **--verbose**

  Prints additional information, including the amount of found homology. Apply multiple times for extra verboseness.

- **-h**, **--help**

  Prints the synopsis and an explanation of available options.

- **--version**

  Outputs version information and acknowledgments.

## COPYRIGHT

Copyright © 2017 - 2023 Fabian Klötzl License GPLv3+: GNU GPL version 3 or later.\
 This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at \<http://gnu.org/licenses/gpl.html\>.

## ACKNOWLEDGMENTS

1\) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.\
 2\) SA construction: Mori, Y. (2005). Short description of improved two-stage suffix sorting algorithm.\
 3\) Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies 4) Phylonium: Klötzl, F. and Haubold, B. (2020). Phylonium: Fast Estimation of Evolutionary Distances from Large Samples of Similar Genomes

## BUGS

### Reporting Bugs

Please report bugs to \<fabian-phylonium@kloetzl.info\>.