---
name: "alf"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alf"
---

# alf(1)

Alignment free sequence comparison

## NAME

alf - Alignment free sequence comparison

## SYNOPSIS

**alf** \[*OPTIONS*\] **-i** *IN.FASTA* \[**-o** *OUT.TXT*\]

## DESCRIPTION

Compute pairwise similarity of sequences using alignment-free methods in *IN.FASTA* and write out tab-delimited matrix with pairwise scores to *OUT.TXT*.

## OPTIONS

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

  Display the help message.

- **--version**

  Display version information.

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

  When given, details about the progress are printed to the screen.

### Input / Output:

- **-i**, **--input-file** *INPUT\_FILE*

  Name of the multi-FASTA input file. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.gbk\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, *.embl\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression.

- **-o**, **--output-file** *OUTPUT\_FILE*

  Name of the file to which the tab-delimtied matrix with pairwise scores will be written to.  Default is to write to stdout. Valid filetype is: *.alf\[.\*\]*, where \* is any of the following extensions: *tsv* for transparent (de)compression.

### General Algorithm Parameters:

- **-m**, **--method** *STRING*

  Select method to use. One of *N2*, *D2*, *D2Star*, and *D2z*. Default: *N2*.

- **-k**, **--k-mer-size** *INTEGER*

  Size of the k-mers. Default: *4*.

- **-mo**, **--bg-model-order** *INTEGER*

  Order of background Markov Model. Default: *1*.

### N2 Algorithm Parameters:

- **-rc**, **--reverse-complement** *STRING*

  Which strand to score.  Use *both\_strands* to score both strands simultaneously. One of *input*, *both\_strands*, *mean*, *min*, and *max*. Default: *input*.

- **-mm**, **--mismatches** *INTEGER*

  Number of mismatches, one of *0* and *1*.  When *1* is used, N2 uses the k-mer-neighbour with one mismatch. Default: *0*.

- **-mmw**, **--mismatch-weight** *DOUBLE*

  Real-valued weight of counts for words with mismatches. Default: *0.1*.

- **-kwf**, **--k-mer-weights-file** *OUTPUT\_FILE*

  Print k-mer weights for every sequence to this file if given. Valid filetype is: *.txt*.

## CONTACT AND REFERENCES

- For questions or comments, contact:

  Jonathan Goeke \<goeke@molgen.mpg.de\>

- Please reference the following publication if you used ALF or the N2 method for your analysis:

  Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. Estimation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts. Bioinformatics (2012).

- Project Homepage:

  http://www.seqan.de/projects/alf