phylonium - rapidly estimate evolutionary distances

       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

ReportingBugs
       Please report bugs to <fabian-phylonium@kloetzl.info>.

1.7                                                2023-03-16                                       PHYLONIUM(1)

       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>.

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.

       phylonium - rapidly estimate evolutionary distances

-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.

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

       -rFILE
              Define the reference sequence.

       -tINT, --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.

       -pFILE
              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.

       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.

phylonium [OPTIONS...] FILES...