NAME

       andi - estimates evolutionary distance

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 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

       -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.

       --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 sequences per file as a single genome. In this mode at  least  one
              filename  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 independent 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', or 'Kimura'. 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), 'always', or 'never'.

       -t INT, --threads=INT
              The number of threads to be used; by default, all available processors 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 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 © 2014 - 2017 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)  andi:  Haubold,  B.  Klötzl,  F.  and  Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of
       evolutionary distances between closely related genomes
       2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements,
       and Phylogenetic Reconstruction. pp 118f.
       3)  SA  construction:  Mori, Y. (2005). Short description of improved two-stage suffix sorting algorithm.
       http://homepage3.nifty.com/wpage/software/itssort.txt
       4) Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies

BUGS

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