xenial (1) andi.1.gz

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NAME
       andi - estimates evolutionary distance


SYNOPSIS
       andi [-jlv] [-b INT] [-p FLOAT] [-m MODEL] [-t INT] 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. (see below).


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, --bootstrap <INT>
              Compute multiple distance matrices, with n-1 bootstrapped from the first. See the paper  Klötzl  &
              Haubold (2016, in review) for a detailed explanation.

       -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 <Raw|JC|Kimura>
              Different models of nucleotide evolution are supported. By default the Jukes-Cantor correction  is
              used.

       -p <FLOAT>
              Significance of an anchor pair; default: 0.05.

       -t <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.

       -v, --verbose
              Prints additional information. Apply multiple times for extra verboseness.

       -h, --help
              Prints the synopsis and an explanation of available options.

       --version
              Outputs version information and acknowledgments.


       Copyright © 2014, 2015 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


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