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>.