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ANDI(1) 			   andi manual				 ANDI(1)

NAME
     andi - estimates evolutionary distances

SYNOPSIS
     andi [OPTIONS...] FILES...

DESCRIPTION
     andi  estimates  the evolutionary distance between closely related genomes.
     For this andi reads the input sequences from FASTA files and  computes  the
     pairwise  anchor  distance. The idea behind this is explained in a paper by
     Haubold et al. (2015).

OUTPUT
     The output is a symmetrical distance matrix in PHYLIP format, with each en-
     try 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 techni-
     cal 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
     -b INT, --bootstrap=INT
	    Compute multiple distance matrices, with n-1 bootstrapped  from  the
	    first.  See  the  paper KlA<paragraph>tzl & Haubold (2016) for a de-
	    tailed explanation.

     --file-of-filenames=FILE
	    Usually, andi is called with the filenames as commandline arguments.
	    With this option the filenames may also be read from a file  itself,
	    with one name per line. Use a single dash ('-') to read from stdin.

     -j, --join
	    Use  this  mode  if each of your FASTA files represents one assembly
	    with numerous contigs. andi will then treat all of the contained se-
	    quences per file as a single genome. In this mode at least one file-
	    name must be provided via command line arguments. For the output the
	    filename is used to identify each sequence.

     -l, --low-memory
	    In multithreaded mode, andi requires memory linear to the amount  of
	    threads. The low memory mode changes this to a constant demand inde-
	    pendent  from  the used number of threads. Unfortunately, this comes
	    at a significant runtime cost.

     -m MODEL, --model=MODEL
	    Set the nucleotide evolution model to one of 'Raw', 'JC',  'Kimura',
	    'LogDet' or 'ANI'. By default the Jukes-Cantor correction is used.

     -p FLOAT
	    Significance of an anchor; default: 0.025.

     --progress[=WHEN]
	    Print  a progress bar. WHEN can be 'auto' (default if omitted), 'al-
	    ways', or 'never'.

     -t INT, --threads=INT
	    The number of threads to be used; by default, all available  proces-
	    sors are used.
	    Multithreading  is	only  available if andi was compiled with OpenMP
	    support.

     --truncate-names
	    By default andi outputs the  full  names  of  sequences,  optionally
	    padded  with  spaces, if they are shorter than ten characters. Names
	    longer than ten characters may  lead  to  problems	with  downstream
	    tools. With this switch names will be truncated.

     -v, --verbose
	    Prints  additional information, including the amount of found homol-
	    ogy. 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 (C) 2014 - 2026 Fabian KlA<paragraph>tzl 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)  andi:	Haubold,  B.  KlA<paragraph>tzl, F. and Pfaffelhuber, P. (2015).
     andi: Fast  and  accurate	estimation  of	evolutionary  distances  between
     closely related genomes, Bioinformatics 31.8.
     2)  Algorithms:  Ohlebusch,  E. (2013). Bioinformatics Algorithms. Sequence
     Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
     3) SA construction: Mori, Y. (2005). libdivsufsort, unpublished.
     4) Bootstrapping: KlA<paragraph>tzl, F. and  Haubold,  B.	(2016).  Support
     Values for Genome Phylogenies, Life 6.1.

BUGS
   Reporting Bugs
     Please	report	   bugs     to	   <kloetzl@evolbio.mpg.de>	or    at
     <https://github.com/EvolBioInf/andi>.

1.15				   2026-01-16				 ANDI(1)
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